diff --git a/.gitignore b/.gitignore index 23066e6..2981502 100644 --- a/.gitignore +++ b/.gitignore @@ -4,4 +4,20 @@ results* .nextflow* work singularity_img/ -vcfs/ \ No newline at end of file +vcfs/ +client-state/ +sessions/ +projects_settings/ +results/ +input/exon_testdata +input/ge +input/GTEX_blood_ge +input/lc_testdata +input/tx_testdata +input/txrev_testdata +sbatch_runs/* +input/* +temp_debug +.venv/ +EDA/* +test_data_legacy/* \ No newline at end of file diff --git a/bin/generate_leafcutter_plot_data.R b/bin/generate_leafcutter_plot_data.R index 8483e5f..8f842da 100644 --- a/bin/generate_leafcutter_plot_data.R +++ b/bin/generate_leafcutter_plot_data.R @@ -21,8 +21,8 @@ option_list <- list( help="The selected qtl_group in the study", metavar = "type"), make_option(c("-v", "--vcf_file"), type="character", default=NULL, help="TPM quantile TSV file with phenotype_id column", metavar = "type"), - make_option(c("-b", "--bigwig_path"), type="character", default=NULL, - help="Path to the bigwig files", metavar = "type"), + make_option(c("-c", "--coverage_parquet"), type="character", default=NULL, + help="Path to the coverage parquet file", metavar = "type"), make_option(c("-m", "--mane_transcript_gene_map"), type="character", default=NULL, help="Path to the MANE transcripts of genes map file", metavar = "type"), make_option(c("-g", "--gtf_file"), type="character", default=NULL, @@ -146,7 +146,7 @@ sample_meta_path = opt$s phenotype_meta_path = opt$p qtl_group_in = opt$q vcf_file_path = opt$v -bigwig_files_path = opt$b +coverage_parquet_path = opt$c mane_transcript_gene_map_file = opt$m tpm_matrix_path = opt$tpm_matrix gtf_file_path = opt$g @@ -162,7 +162,7 @@ message("######### susie_file_path : ", susie_file_path) message("######### sample_meta_path : ", sample_meta_path) message("######### phenotype_meta_path: ", phenotype_meta_path) message("######### vcf_file_path : ", vcf_file_path) -message("######### bigwig_files_path : ", bigwig_files_path) +message("######### coverage_parquet : ", coverage_parquet_path) message("######### mane_map_file_path : ", mane_transcript_gene_map_file) message("######### gtf_file_path : ", gtf_file_path) message("######### scaling_fct_path : ", scaling_factors_path) @@ -277,21 +277,13 @@ for (index in 1:nrow(highest_pip_vars_per_cs)) { var_genotype <- sample_meta_clean %>% left_join(var_genotype, by = "genotype_id") - bigwig_files <- list.files(bigwig_files_path, full.names = T) - - track_data_study <- data.frame(file_name = (gsub(pattern = paste0(bigwig_files_path, "/"), replacement = "", x = bigwig_files, fixed = T)), - bigWig = bigwig_files) - - track_data_study <- track_data_study %>% - dplyr::mutate(sample_id = gsub(pattern = ".bigwig", replacement = "", x = file_name)) %>% - dplyr::filter(sample_id %in% sample_meta_clean$sample_id) - - track_data_study <-track_data_study %>% - dplyr::left_join(var_genotype %>% dplyr::select(sample_id, qtl_group, DS), by = c("sample_id")) %>% + track_data_study <- var_genotype %>% + dplyr::select(sample_id, qtl_group, DS) %>% dplyr::left_join(scaling_factor_data) %>% dplyr::rename(scaling_factor = scaling_factors) %>% dplyr::mutate(track_id = qtl_group) %>% dplyr::mutate(colour_group = as.character(DS)) %>% + dplyr::mutate(bigWig = "") %>% dplyr::select(sample_id, scaling_factor, bigWig, track_id, colour_group, qtl_group) %>% dplyr::filter(qtl_group==qtl_group_in) @@ -354,7 +346,8 @@ for (index in 1:nrow(highest_pip_vars_per_cs)) { coverage_data_list = tryCatch(wiggleplotr::extractCoverageData(exons = exons_to_plot, cdss = exon_cdss_to_plot, # Does var will be default NULL if not stated? plot_fraction = 0.2, - track_data = track_data_study), + track_data = track_data_study, + coverage_ranges_pq = coverage_parquet_path), error = function(e) { message(" ## Problem with generating coverage_data wiggleplotr") message(e) @@ -408,6 +401,10 @@ for (index in 1:nrow(highest_pip_vars_per_cs)) { track_data_study_box <- track_data_study_box %>% dplyr::left_join(tpm_exp_df_oi, by = c("sample_id", "intron_id")) + # Remove samples present in expression matrix but missing from metadata-filtered sample set + track_data_study_box <- track_data_study_box %>% + dplyr::filter(!is.na(snp_id)) + nom_cc_sumstats_variant_phenotype_id <- read_and_filter_parquet( file_list = ss_oi$nominal_cc_path[[1]], variant_to_match = ss_oi$variant, diff --git a/bin/generate_plot_exon_data.R b/bin/generate_plot_exon_data.R index fafc7a8..0d438f1 100644 --- a/bin/generate_plot_exon_data.R +++ b/bin/generate_plot_exon_data.R @@ -13,8 +13,8 @@ option_list <- list( help="The selected qtl_group in the study", metavar = "type"), make_option(c("-v", "--vcf_file"), type="character", default=NULL, help="TPM quantile TSV file with phenotype_id column", metavar = "type"), - make_option(c("-b", "--bigwig_path"), type="character", default=NULL, - help="Path to the bigwig files", metavar = "type"), + make_option(c("-c", "--coverage_parquet"), type="character", default=NULL, + help="Path to the coverage parquet file", metavar = "type"), make_option(c("-m", "--mane_transcript_gene_map"), type="character", default=NULL, help="Path to the MANE transcripts of genes map file", metavar = "type"), make_option(c("-g", "--gtf_file"), type="character", default=NULL, @@ -134,7 +134,7 @@ sample_meta_path = opt$s phenotype_meta_path = opt$p qtl_group_in = opt$q vcf_file_path = opt$v -bigwig_files_path = opt$b +coverage_parquet_path = opt$c mane_transcript_gene_map_file = opt$m gtf_file_path = opt$g norm_usage_matrix_path = opt$u @@ -151,7 +151,7 @@ message("######### susie_file_path : ", susie_file_path) message("######### sample_meta_path : ", sample_meta_path) message("######### phenotype_meta_path: ", phenotype_meta_path) message("######### vcf_file_path : ", vcf_file_path) -message("######### bigwig_files_path : ", bigwig_files_path) +message("######### coverage_parquet : ", coverage_parquet_path) message("######### mane_map_file_path : ", mane_transcript_gene_map_file) message("######### gtf_file_path : ", gtf_file_path) message("######### tpm_matrix : ", tpm_matrix_path) @@ -284,21 +284,13 @@ for (index in 1:nrow(highest_pip_vars_per_cs)) { var_genotype <- sample_meta_clean %>% left_join(var_genotype, by = "genotype_id") - bigwig_files <- list.files(bigwig_files_path, full.names = T) - - track_data_study <- data.frame(file_name = (gsub(pattern = paste0(bigwig_files_path, "/"), replacement = "", x = bigwig_files, fixed = T)), - bigWig = bigwig_files) - - track_data_study <- track_data_study %>% - dplyr::mutate(sample_id = gsub(pattern = ".bigwig", replacement = "", x = file_name)) %>% - dplyr::filter(sample_id %in% sample_meta_clean$sample_id) - - track_data_study <-track_data_study %>% - dplyr::left_join(var_genotype %>% dplyr::select(sample_id, qtl_group, DS), by = c("sample_id")) %>% + track_data_study <- var_genotype %>% + dplyr::select(sample_id, qtl_group, DS) %>% dplyr::left_join(scaling_factor_data) %>% dplyr::rename(scaling_factor = scaling_factors) %>% dplyr::mutate(track_id = qtl_group) %>% dplyr::mutate(colour_group = as.character(DS)) %>% + dplyr::mutate(bigWig = "") %>% dplyr::select(sample_id, scaling_factor, bigWig, track_id, colour_group, qtl_group) %>% dplyr::filter(qtl_group==qtl_group_in) @@ -368,7 +360,8 @@ for (index in 1:nrow(highest_pip_vars_per_cs)) { coverage_data_list = tryCatch(wiggleplotr::extractCoverageData(exons = exons_to_plot, cdss = exon_cdss_to_plot, plot_fraction = 0.2, - track_data = track_data_study), + track_data = track_data_study, + coverage_ranges_pq = coverage_parquet_path), error = function(e) { message(" ## Problem with generating coverage_data wiggleplotr") message(e) @@ -414,6 +407,10 @@ for (index in 1:nrow(highest_pip_vars_per_cs)) { track_data_study_box <- track_data_study_box %>% dplyr::left_join(tpm_exp_df_oi, by = c("sample_id", "tx_id")) + # Remove samples present in expression matrix but missing from metadata-filtered sample set + track_data_study_box <- track_data_study_box %>% + dplyr::filter(!is.na(snp_id)) + message(" ## Reading nominal summary stats with seqminer") # Keep only 1 rsid per variant per molecular_trait_id diff --git a/bin/generate_plot_ge_data.R b/bin/generate_plot_ge_data.R index 17d554d..19da5f8 100644 --- a/bin/generate_plot_ge_data.R +++ b/bin/generate_plot_ge_data.R @@ -18,8 +18,8 @@ option_list <- list( help="The selected qtl_group in the study", metavar = "type"), make_option(c("-v", "--vcf_file"), type="character", default=NULL, help="TPM quantile TSV file with phenotype_id column", metavar = "type"), - make_option(c("-b", "--bigwig_path"), type="character", default=NULL, - help="Path to the bigwig files", metavar = "type"), + make_option(c("-c", "--coverage_parquet"), type="character", default=NULL, + help="Path to the coverage parquet file", metavar = "type"), make_option(c("-m", "--mane_transcript_gene_map"), type="character", default=NULL, help="Path to the MANE transcripts of genes map file", metavar = "type"), make_option(c("-g", "--gtf_file"), type="character", default=NULL, @@ -78,7 +78,7 @@ prepareTranscriptStructureForPlotting <- function(exon_ranges, cds_ranges, trans filter_trait_matrix <- function(unique_trait_ids, trait_matrix_pq_file) { trait_dataset <- open_dataset(trait_matrix_pq_file) filtered_traits_dataset <- trait_dataset %>% - filter(phenotype_id %in% unique_trait_ids) + dplyr::filter(phenotype_id %in% unique_trait_ids) traits_df <- collect(filtered_traits_dataset) return(traits_df) } @@ -109,7 +109,7 @@ read_and_filter_parquet <- function(file_list, variant_to_match, phenotype_id) { dataset <- open_dataset(file_name) filtered_data <- dataset %>% - filter(variant == variant_to_match & gene_id == phenotype_id) %>% + dplyr::filter(variant == variant_to_match & gene_id == phenotype_id) %>% collect() if (nrow(filtered_data) > 0) { @@ -126,7 +126,7 @@ susie_file_path = opt$f sample_meta_path = opt$s qtl_group_in = opt$q vcf_file_path = opt$v -bigwig_files_path = opt$b +coverage_parquet_path = opt$c mane_transcript_gene_map_file = opt$m gtf_file_path = opt$g norm_usage_matrix_path = opt$u @@ -135,13 +135,27 @@ scaling_factors_path = opt$div_scaling_factors vcf_sample_bad_symbol = opt$vcf_sample_bad_symbol vcf_sample_replacement_symbol = opt$vcf_sample_replacement_symbol +# base_path <- "~/alasoo_lab/coverage_plot_fixer/work_dir/" +# +# qtl_group_in <- "LCL" +# susie_file_path <- paste0(base_path, "QTD000764_LCL_ge_1_1.parquet") +# sample_meta_path <- paste0(base_path, "MAGE_McCoy_2023_QC_all_samples.tsv") +# vcf_file_path <- paste0(base_path, "MAGE_with_SV_20220422_3202.filtered_chr5_96894474-96991959_test_samples.vcf.gz") +# mane_transcript_gene_map_file <- paste0(base_path, "MANE_transcript_gene_map.txt") +# gtf_file_path <- paste0(base_path, "Homo_sapiens.GRCh38.105.gtf") +# scaling_factors_path <- paste0(base_path, "MAGE.LCL.scaling_factors.tsv.gz") +# norm_usage_matrix_path <- paste0(base_path, "MAGE.parquet") +# tpm_matrix_path <- paste0(base_path, "MAGE_TPM.parquet") +# coverage_parquet_path <- paste0(base_path, "MAGE_bigwig_single.parquet") + + message("######### Options: ######### ") message("######### Working Directory : ", getwd()) message("######### qtl_group : ", qtl_group_in) message("######### susie_file_path : ", susie_file_path) message("######### sample_meta_path : ", sample_meta_path) message("######### vcf_file_path : ", vcf_file_path) -message("######### bigwig_files_path : ", bigwig_files_path) +message("######### coverage_parquet : ", coverage_parquet_path) message("######### mane_map_file_path : ", mane_transcript_gene_map_file) message("######### gtf_file_path : ", gtf_file_path) message("######### scaling_fct_path : ", scaling_factors_path) @@ -197,10 +211,6 @@ norm_exp_df <- filter_trait_matrix(trait_ids, norm_usage_matrix_path) tpm_exp_df <- filter_trait_matrix(trait_ids, tpm_matrix_path) - -###norm_exp_df <- readr::read_tsv(norm_usage_matrix_path) - - message(" ## Reading scaling_factors file") scaling_factor_data <- readr::read_tsv(scaling_factors_path, col_types = "cd") @@ -262,25 +272,16 @@ for (index in 1:nrow(highest_pip_vars_per_cs)) { var_genotype <- sample_meta_clean %>% left_join(var_genotype, by = "genotype_id") - bigwig_files <- list.files(bigwig_files_path, full.names = T) - - track_data_study <- data.frame(file_name = (gsub(pattern = paste0(bigwig_files_path, "/"), replacement = "", x = bigwig_files, fixed = T)), - bigWig = bigwig_files) - - track_data_study <- track_data_study %>% - dplyr::mutate(sample_id = gsub(pattern = ".bigwig", replacement = "", x = file_name)) %>% - dplyr::filter(sample_id %in% sample_meta_clean$sample_id) - - track_data_study <-track_data_study %>% - dplyr::left_join(var_genotype %>% dplyr::select(sample_id, qtl_group, DS), by = c("sample_id")) %>% + track_data_study <- var_genotype %>% + dplyr::select(sample_id, qtl_group, DS) %>% dplyr::left_join(scaling_factor_data) %>% dplyr::rename(scaling_factor = scaling_factors) %>% dplyr::mutate(track_id = qtl_group) %>% dplyr::mutate(colour_group = as.character(DS)) %>% + dplyr::mutate(bigWig = "") %>% dplyr::select(sample_id, scaling_factor, bigWig, track_id, colour_group, qtl_group) %>% dplyr::filter(qtl_group==qtl_group_in) - start_time <- time_here(prev_time = start_time, message_text = " >> prepared track_data_study in: ") nom_exon_cc_sumstats_all <- read_and_filter_parquet( @@ -331,7 +332,8 @@ for (index in 1:nrow(highest_pip_vars_per_cs)) { coverage_data_list = tryCatch(wiggleplotr::extractCoverageData(exons = exons_to_plot, cdss = exon_cdss_to_plot, plot_fraction = 0.2, - track_data = track_data_study), + track_data = track_data_study, + coverage_ranges_pq = coverage_parquet_path), error = function(e) { message(" ## Problem with generating coverage_data wiggleplotr") message(e) @@ -369,6 +371,10 @@ for (index in 1:nrow(highest_pip_vars_per_cs)) { dplyr::left_join(track_data_study_box, by = "sample_id") track_data_study_box <- track_data_study_box %>% dplyr::left_join(tpm_exp_df_oi, by = c("sample_id", "tx_id")) + + # Remove samples present in expression matrix but missing from metadata-filtered sample set + track_data_study_box <- track_data_study_box %>% + dplyr::filter(!is.na(snp_id)) message(" ## Filter nominal summstats") @@ -425,4 +431,4 @@ for (index in 1:nrow(highest_pip_vars_per_cs)) { nom_exon_cc_sumstats_filt <- nom_exon_cc_sumstats_filt %>% mutate(rsid = stringr::str_trim(rsid)) arrow::write_parquet(nom_exon_cc_sumstats_filt, file.path(output_path, paste0("nom_exon_cc_", signal_name, ".parquet"))) -} \ No newline at end of file +} diff --git a/bin/generate_tx_plot_data.R b/bin/generate_tx_plot_data.R index e836220..46017a6 100644 --- a/bin/generate_tx_plot_data.R +++ b/bin/generate_tx_plot_data.R @@ -20,8 +20,8 @@ option_list <- list( help="The selected qtl_group in the study", metavar = "type"), make_option(c("-v", "--vcf_file"), type="character", default=NULL, help="TPM quantile TSV file with phenotype_id column", metavar = "type"), - make_option(c("-b", "--bigwig_path"), type="character", default=NULL, - help="Path to the bigwig files", metavar = "type"), + make_option(c("-c", "--coverage_parquet"), type="character", default=NULL, + help="Path to the coverage parquet file", metavar = "type"), make_option(c("-m", "--mane_transcript_gene_map"), type="character", default=NULL, help="Path to the MANE transcripts of genes map file", metavar = "type"), make_option(c("-g", "--gtf_file"), type="character", default=NULL, @@ -128,7 +128,7 @@ sample_meta_path = opt$s phenotype_meta_path = opt$p qtl_group_in = opt$q vcf_file_path = opt$v -bigwig_files_path = opt$b +coverage_parquet_path = opt$c mane_transcript_gene_map_file = opt$m gtf_file_path = opt$g tx_gtf_file_path = opt$tx_gtf_file @@ -145,7 +145,7 @@ message("######### susie_file_path : ", susie_file_path) message("######### sample_meta_path : ", sample_meta_path) message("######### phenotype_meta_path: ", phenotype_meta_path) message("######### vcf_file_path : ", vcf_file_path) -message("######### bigwig_files_path : ", bigwig_files_path) +message("######### coverage_parquet : ", coverage_parquet_path) message("######### mane_map_file_path : ", mane_transcript_gene_map_file) message("######### gtf_file_path : ", gtf_file_path) message("######### scaling_fct_path : ", scaling_factors_path) @@ -268,21 +268,13 @@ for (index in 1:nrow(highest_pip_vars_per_cs)) { var_genotype <- sample_meta_clean %>% left_join(var_genotype, by = "genotype_id") - bigwig_files <- list.files(bigwig_files_path, full.names = T) - - track_data_study <- data.frame(file_name = (gsub(pattern = paste0(bigwig_files_path, "/"), replacement = "", x = bigwig_files, fixed = T)), - bigWig = bigwig_files) - - track_data_study <- track_data_study %>% - dplyr::mutate(sample_id = gsub(pattern = ".bigwig", replacement = "", x = file_name)) %>% - dplyr::filter(sample_id %in% sample_meta_clean$sample_id) - - track_data_study <-track_data_study %>% - dplyr::left_join(var_genotype %>% dplyr::select(sample_id, qtl_group, DS), by = c("sample_id")) %>% + track_data_study <- var_genotype %>% + dplyr::select(sample_id, qtl_group, DS) %>% dplyr::left_join(scaling_factor_data) %>% dplyr::rename(scaling_factor = scaling_factors) %>% dplyr::mutate(track_id = qtl_group) %>% dplyr::mutate(colour_group = as.character(DS)) %>% + dplyr::mutate(bigWig = "") %>% dplyr::select(sample_id, scaling_factor, bigWig, track_id, colour_group, qtl_group) %>% dplyr::filter(qtl_group==qtl_group_in) @@ -345,7 +337,8 @@ for (index in 1:nrow(highest_pip_vars_per_cs)) { coverage_data_list = tryCatch(wiggleplotr::extractCoverageData(exons = exons_to_plot, cdss = exon_cdss_to_plot, plot_fraction = 0.2, - track_data = track_data_study), + track_data = track_data_study, + coverage_ranges_pq = coverage_parquet_path), error = function(e) { message(" ## Problem with generating coverage_data wiggleplotr") message(e) @@ -390,6 +383,10 @@ for (index in 1:nrow(highest_pip_vars_per_cs)) { track_data_study_box <- track_data_study_box %>% dplyr::left_join(tpm_exp_df_oi, by = c("sample_id", "tx_id")) + # Remove samples present in expression matrix but missing from metadata-filtered sample set + track_data_study_box <- track_data_study_box %>% + dplyr::filter(!is.na(snp_id)) + message(" ## Reading nominal summary stats with seqminer") nom_cc_sumstats_variant_phenotype_id <- read_and_filter_parquet( file_list = ss_oi$nominal_cc_path[[1]], diff --git a/bin/generate_txrev_plot_data.R b/bin/generate_txrev_plot_data.R index b5789c6..4a78805 100644 --- a/bin/generate_txrev_plot_data.R +++ b/bin/generate_txrev_plot_data.R @@ -20,8 +20,8 @@ option_list <- list( help="The selected qtl_group in the study", metavar = "type"), make_option(c("-v", "--vcf_file"), type="character", default=NULL, help="TPM quantile TSV file with phenotype_id column", metavar = "type"), - make_option(c("-b", "--bigwig_path"), type="character", default=NULL, - help="Path to the bigwig files", metavar = "type"), + make_option(c("-c", "--coverage_parquet"), type="character", default=NULL, + help="Path to the coverage parquet file", metavar = "type"), make_option(c("-m", "--mane_transcript_gene_map"), type="character", default=NULL, help="Path to the MANE transcripts of genes map file", metavar = "type"), make_option(c("-g", "--gtf_file"), type="character", default=NULL, @@ -140,7 +140,7 @@ sample_meta_path = opt$s phenotype_meta_path = opt$p qtl_group_in = opt$q vcf_file_path = opt$v -bigwig_files_path = opt$b +coverage_parquet_path = opt$c mane_transcript_gene_map_file = opt$m gtf_file_path = opt$g txrev_gtf_file_path = opt$txrev_gtf_file @@ -158,7 +158,7 @@ message("######### susie_file_path : ", susie_file_path) message("######### sample_meta_path : ", sample_meta_path) message("######### phenotype_meta_path: ", phenotype_meta_path) message("######### vcf_file_path : ", vcf_file_path) -message("######### bigwig_files_path : ", bigwig_files_path) +message("######### coverage_parquet : ", coverage_parquet_path) message("######### mane_map_file_path : ", mane_transcript_gene_map_file) message("######### gtf_file_path : ", gtf_file_path) message("######### scaling_fct_path : ", scaling_factors_path) @@ -284,21 +284,13 @@ for (index in 1:nrow(highest_pip_vars_per_cs)) { var_genotype <- sample_meta_clean %>% left_join(var_genotype, by = "genotype_id") - bigwig_files <- list.files(bigwig_files_path, full.names = T) - - track_data_study <- data.frame(file_name = (gsub(pattern = paste0(bigwig_files_path, "/"), replacement = "", x = bigwig_files, fixed = T)), - bigWig = bigwig_files) - - track_data_study <- track_data_study %>% - dplyr::mutate(sample_id = gsub(pattern = ".bigwig", replacement = "", x = file_name)) %>% - dplyr::filter(sample_id %in% sample_meta_clean$sample_id) - - track_data_study <-track_data_study %>% - dplyr::left_join(var_genotype %>% dplyr::select(sample_id, qtl_group, DS), by = c("sample_id")) %>% + track_data_study <- var_genotype %>% + dplyr::select(sample_id, qtl_group, DS) %>% dplyr::left_join(scaling_factor_data) %>% dplyr::rename(scaling_factor = scaling_factors) %>% dplyr::mutate(track_id = qtl_group) %>% dplyr::mutate(colour_group = as.character(DS)) %>% + dplyr::mutate(bigWig = "") %>% dplyr::select(sample_id, scaling_factor, bigWig, track_id, colour_group, qtl_group) %>% dplyr::filter(qtl_group==qtl_group_in) @@ -364,7 +356,8 @@ for (index in 1:nrow(highest_pip_vars_per_cs)) { coverage_data_list = tryCatch(wiggleplotr::extractCoverageData(exons = exons_to_plot, cdss = exon_cdss_to_plot, plot_fraction = 0.2, - track_data = track_data_study), + track_data = track_data_study, + coverage_ranges_pq = coverage_parquet_path), error = function(e) { message(" ## Problem with generating coverage_data wiggleplotr") message(e) @@ -409,6 +402,10 @@ for (index in 1:nrow(highest_pip_vars_per_cs)) { track_data_study_box <- track_data_study_box %>% dplyr::left_join(tpm_exp_df_oi, by = c("sample_id", "intron_id")) + # Remove samples present in expression matrix but missing from metadata-filtered sample set + track_data_study_box <- track_data_study_box %>% + dplyr::filter(!is.na(snp_id)) + nom_cc_sumstats_variant_phenotype_id <- read_and_filter_parquet( file_list = ss_oi$nominal_cc_path[[1]], variant_to_match = ss_oi$variant, diff --git a/conf/base.config b/conf/base.config index a815613..436f0a9 100644 --- a/conf/base.config +++ b/conf/base.config @@ -14,10 +14,11 @@ process { memory = { check_max( 8.GB * task.attempt, 'memory' ) } time = { check_max( 4.h * task.attempt, 'time' ) } - maxRetries = 1 + maxRetries = 3 maxErrors = '-1' - errorStrategy = { task.exitStatus in [140,143,137,104,134,139] ? 'retry' : 'terminate' } + // errorStrategy = { task.exitStatus in [140,143,137,104,134,139] ? 'retry' : 'ignore' } + errorStrategy = "retry" // errorStrategy = 'finish' // Process-specific resource requirements @@ -49,8 +50,8 @@ process { } withLabel:generate_plot_data { cpus = { check_max( 1 * task.attempt, 'cpus' ) } - memory = { check_max( 10.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } + time = { check_max( 12.h * task.attempt, 'time' ) } } } diff --git a/conf/tartu_hpc.config b/conf/tartu_hpc.config index a00f858..19d6cf1 100644 --- a/conf/tartu_hpc.config +++ b/conf/tartu_hpc.config @@ -17,7 +17,7 @@ singularity { executor { name = 'slurm' - queueSize = 1200 + queueSize = 300 submitRateLimit = 1 } @@ -30,6 +30,6 @@ params { mane_transcript_gene_map = "/gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/MANE_transcript_gene_map.txt" mane_gtf_file = "/gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/Homo_sapiens.GRCh38.105.gtf" tx_gtf_file = "/gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/GENCODE/gencode.v39.annotation.nochr.gtf" - txrev_gtf_file = "/gpfs/helios/home/a82371/eQTL_plot_data/eqtl_plot_data_generator/data/txrevise.all.gff3" + txrev_gtf_file = "/gpfs/helios/projects/otar2069/coverage_plot_data/txrevise.all.gff3" } \ No newline at end of file diff --git a/data/wf_modifications.txt b/data/wf_modifications.txt deleted file mode 100644 index bb78986..0000000 --- a/data/wf_modifications.txt +++ /dev/null @@ -1,67 +0,0 @@ -1. The preparation of batches script (previously located at /bin/prepare_batches.R) has been updated. Rows without position information are now filtered out later in the process than before. -e.g susie_high_pip_with_gene <- data.frame( - cs_id = c("A", "A", "A", "B", "B", "B", "C", "C"), - pip = c(0.8, 0.5, 0.9, 0.6, 0.7, 0.4, 0.3, 0.2), - position = c(100, 200, NA, 300, 400, NA, 500, NA) -) -highest_pip_vars_per_cs <- susie_high_pip_with_gene %>% - dplyr::group_by(cs_id) %>% - dplyr::arrange(-pip) %>% - dplyr::slice(1) %>% - dplyr::ungroup() %>% - dplyr::filter(!is.na(position)) yields: # A tibble: 2 × 3 - cs_id pip position - -1 B 0.7 400 -2 C 0.3 500 - -import polars as pl - -data = { - "cs_id": ["A", "A", "A", "B", "B", "B", "C", "C"], - "pip": [0.8, 0.5, 0.9, 0.6, 0.7, 0.4, 0.3, 0.2], - "position": [100, 200, None, 300, 400, None, 500, None], -} - -df_credible_sets = pl.DataFrame(data) - -highest_pip_vars_per_cs = ( - df_credible_sets - .filter(pl.col("position").is_not_null()) - .sort(["cs_id", "pip"], descending=[False, True]) - .group_by("cs_id") - .agg(pl.all().first()) -) yields: shape: (3, 3) -┌───────┬─────┬──────────┐ -│ cs_id ┆ pip ┆ position │ -│ --- ┆ --- ┆ --- │ -│ str ┆ f64 ┆ i64 │ -╞═══════╪═════╪══════════╡ -│ B ┆ 0.7 ┆ 400 │ -│ A ┆ 0.8 ┆ 100 │ -│ C ┆ 0.3 ┆ 500 │ -└───────┴─────┴──────────┘ - -2. When the nom_exon_cc_sumstats_ss_oi variable is empty, a NULL value is passed to cdss to avoid errors during the wiggleplotr::extractCoverageData call: coverage_data_list = tryCatch(wiggleplotr::extractCoverageData(exons = exons_to_plot, - cdss = exon_cdss_to_plot, # NULL? - plot_fraction = 0.2, - track_data = track_data_study), - error = function(e) { - message(" ## Problem with generating coverage_data wiggleplotr") - message(e) - }) -This is done to avoide the error: index: 1, exon_phenotype_id: ENSG00000144711.16_3_12908349_12908525, variant: chr3_13075916_C_T - ## Preparing Track Data - Joining with `by = join_by(sample_id)` - Error in stop_if_wrong_length("'seqnames'", ans_len) : - 'seqnames' must have the length of the object to construct (1) or - length 1 - Calls: -> new_GRanges -> stop_if_wrong_length - Execution halted -3. R scripts no longer generate tar-zipped files; instead, they create directories to eliminate the need for repacking during the sqlite file generation process. -4. Updated the leafcutter script to modify signal_name naming conventions by replacing "&" with "__", as the "&" symbol caused issues in bash. - - -TODO: -* Fix genotype_id names check and replacment in R scripts. -* Create small testdata for git repo. diff --git a/input/GTEx_V10_all/GTEx_V10_input.tsv b/input/GTEx_V10_all/GTEx_V10_input.tsv new file mode 100644 index 0000000..550176a --- /dev/null +++ b/input/GTEx_V10_all/GTEx_V10_input.tsv @@ -0,0 +1,6 @@ +dataset_id study_id quant_method qtl_group study_name credible_sets_file sample_meta vcf_file coverage_path usage_matrix_norm tpm_matrix exon_summ_stats_files all_summ_stats_files pheno_meta scaling_factors +QTD000116 QTS000015 ge adipose_subcutaneous GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000116/QTD000116.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_adipose_subcutaneous.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/adipose_subcutaneous.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/ge/qtl_group_split_norm/GTEx.adipose_subcutaneous.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/ge/per_million_normalised/GTEx.adipose_subcutaneous.gene_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEX_blood_ge/GTEx_blood_exon_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEX_blood_ge/GTEx_blood_ge_sumstats_files.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/gene_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/ge/per_million_normalised/GTEx.blood.scaling_factors.tsv.gz +QTD000117 QTS000015 exon adipose_subcutaneous GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000117/QTD000117.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_adipose_subcutaneous.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/adipose_subcutaneous.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.adipose_subcutaneous.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/exon/per_million_normalised/GTEx.adipose_subcutaneous.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEX_blood_ge/GTEx_blood_exon_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEX_blood_ge/GTEx_blood_ge_sumstats_files.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/gene_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/ge/per_million_normalised/GTEx.blood.scaling_factors.tsv.gz +QTD000118 QTS000015 tx adipose_subcutaneous GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000118/QTD000118.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_adipose_subcutaneous.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/adipose_subcutaneous.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/tx/qtl_group_split_norm/GTEx.adipose_subcutaneous.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/tx/per_million_normalised/GTEx.adipose_subcutaneous.transcript_usage_TPM_norm.tsv.gz +QTD000119 QTS000015 txrev adipose_subcutaneous GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000119/QTD000119.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_adipose_subcutaneous.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/adipose_subcutaneous.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/txrev/qtl_group_split_norm/GTEx.adipose_subcutaneous.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/txrev/per_million_normalised/GTEx.adipose_subcutaneous.txrevise_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEX_blood_ge/GTEx_blood_exon_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEX_blood_ge/GTEx_blood_ge_sumstats_files.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/gene_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/ge/per_million_normalised/GTEx.blood.scaling_factors.tsv.gz +QTD000120 QTS000015 leafcutter adipose_subcutaneous GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000120/QTD000120.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_adipose_subcutaneous.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/adipose_subcutaneous.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/leafcutter/qtl_group_split_norm/GTEx.adipose_subcutaneous.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/leafcutter/per_million_normalised/GTEx.adipose_subcutaneous.leafcutter_CPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEX_blood_ge/GTEx_blood_exon_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEX_blood_ge/GTEx_blood_ge_sumstats_files.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/gene_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/ge/per_million_normalised/GTEx.blood.scaling_factors.tsv.gz diff --git a/input/GTEx_V10_all/GTEx_V10_input_exon_all.tsv b/input/GTEx_V10_all/GTEx_V10_input_exon_all.tsv new file mode 100644 index 0000000..f9c63c6 --- /dev/null +++ b/input/GTEx_V10_all/GTEx_V10_input_exon_all.tsv @@ -0,0 +1,49 @@ +dataset_id study_id quant_method qtl_group study_name credible_sets_file sample_meta vcf_file coverage_path usage_matrix_norm tpm_matrix exon_summ_stats_files all_summ_stats_files pheno_meta scaling_factors +QTD000117 QTS000015 exon adipose_subcutaneous GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000117/QTD000117.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_adipose_subcutaneous.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/adipose_subcutaneous.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.adipose_subcutaneous.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/exon/per_million_normalised/GTEx.adipose_subcutaneous.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000117_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000117_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/ge/per_million_normalised/GTEx.adipose_subcutaneous.scaling_factors.tsv.gz +QTD000122 QTS000015 exon adipose_visceral GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000122/QTD000122.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_adipose_visceral.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/adipose_visceral.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_visceral/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.adipose_visceral.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_visceral/QTS000015/normalised/exon/per_million_normalised/GTEx.adipose_visceral.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000122_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000122_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_visceral/QTS000015/normalised/ge/per_million_normalised/GTEx.adipose_visceral.scaling_factors.tsv.gz +QTD000127 QTS000015 exon adrenal_gland GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000127/QTD000127.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_adrenal_gland.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/adrenal_gland.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adrenal_gland/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.adrenal_gland.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adrenal_gland/QTS000015/normalised/exon/per_million_normalised/GTEx.adrenal_gland.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000127_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000127_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adrenal_gland/QTS000015/normalised/ge/per_million_normalised/GTEx.adrenal_gland.scaling_factors.tsv.gz +QTD000132 QTS000015 exon artery_aorta GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000132/QTD000132.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_artery_aorta.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/artery_aorta.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_aorta/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.artery_aorta.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_aorta/QTS000015/normalised/exon/per_million_normalised/GTEx.artery_aorta.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000132_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000132_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_aorta/QTS000015/normalised/ge/per_million_normalised/GTEx.artery_aorta.scaling_factors.tsv.gz +QTD000137 QTS000015 exon artery_coronary GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000137/QTD000137.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_artery_coronary.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/artery_coronary.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_coronary/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.artery_coronary.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_coronary/QTS000015/normalised/exon/per_million_normalised/GTEx.artery_coronary.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000137_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000137_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_coronary/QTS000015/normalised/ge/per_million_normalised/GTEx.artery_coronary.scaling_factors.tsv.gz +QTD000142 QTS000015 exon artery_tibial GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000142/QTD000142.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_artery_tibial.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/artery_tibial.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_tibial/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.artery_tibial.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_tibial/QTS000015/normalised/exon/per_million_normalised/GTEx.artery_tibial.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000142_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000142_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_tibial/QTS000015/normalised/ge/per_million_normalised/GTEx.artery_tibial.scaling_factors.tsv.gz +QTD000147 QTS000015 exon brain_amygdala GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000147/QTD000147.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_amygdala.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_amygdala.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_amygdala/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.brain_amygdala.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_amygdala/QTS000015/normalised/exon/per_million_normalised/GTEx.brain_amygdala.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000147_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000147_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_amygdala/QTS000015/normalised/ge/per_million_normalised/GTEx.brain_amygdala.scaling_factors.tsv.gz +QTD000152 QTS000015 exon brain_anterior_cingulate_cortex GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000152/QTD000152.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_anterior_cingulate_cortex.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_anterior_cingulate_cortex.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_anterior_cingulate_cortex/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.brain_anterior_cingulate_cortex.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_anterior_cingulate_cortex/QTS000015/normalised/exon/per_million_normalised/GTEx.brain_anterior_cingulate_cortex.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000152_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000152_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_anterior_cingulate_cortex/QTS000015/normalised/ge/per_million_normalised/GTEx.brain_anterior_cingulate_cortex.scaling_factors.tsv.gz +QTD000157 QTS000015 exon brain_caudate GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000157/QTD000157.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_caudate.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_caudate.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_caudate/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.brain_caudate.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_caudate/QTS000015/normalised/exon/per_million_normalised/GTEx.brain_caudate.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000157_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000157_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_caudate/QTS000015/normalised/ge/per_million_normalised/GTEx.brain_caudate.scaling_factors.tsv.gz +QTD000162 QTS000015 exon brain_cerebellar_hemisphere GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000162/QTD000162.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_cerebellar_hemisphere.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_cerebellar_hemisphere.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_cerebellar_hemisphere/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.brain_cerebellar_hemisphere.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_cerebellar_hemisphere/QTS000015/normalised/exon/per_million_normalised/GTEx.brain_cerebellar_hemisphere.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000162_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000162_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_cerebellar_hemisphere/QTS000015/normalised/ge/per_million_normalised/GTEx.brain_cerebellar_hemisphere.scaling_factors.tsv.gz +QTD000167 QTS000015 exon brain_cerebellum GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000167/QTD000167.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_cerebellum.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_cerebellum.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_cerebellum/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.brain_cerebellum.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_cerebellum/QTS000015/normalised/exon/per_million_normalised/GTEx.brain_cerebellum.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000167_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000167_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_cerebellum/QTS000015/normalised/ge/per_million_normalised/GTEx.brain_cerebellum.scaling_factors.tsv.gz +QTD000172 QTS000015 exon brain_cortex GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000172/QTD000172.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_brain_cortex.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_cortex.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_cortex/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.brain_cortex.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_cortex/QTS000015/normalised/exon/per_million_normalised/GTEx.brain_cortex.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000172_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000172_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_cortex/QTS000015/normalised/ge/per_million_normalised/GTEx.brain_cortex.scaling_factors.tsv.gz +QTD000177 QTS000015 exon brain_frontal_cortex GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000177/QTD000177.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_frontal_cortex.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_frontal_cortex.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_frontal_cortex/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.brain_frontal_cortex.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_frontal_cortex/QTS000015/normalised/exon/per_million_normalised/GTEx.brain_frontal_cortex.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000177_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000177_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_frontal_cortex/QTS000015/normalised/ge/per_million_normalised/GTEx.brain_frontal_cortex.scaling_factors.tsv.gz +QTD000182 QTS000015 exon brain_hippocampus GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000182/QTD000182.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_hippocampus.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_hippocampus.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_hippocampus/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.brain_hippocampus.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_hippocampus/QTS000015/normalised/exon/per_million_normalised/GTEx.brain_hippocampus.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000182_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000182_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_hippocampus/QTS000015/normalised/ge/per_million_normalised/GTEx.brain_hippocampus.scaling_factors.tsv.gz +QTD000187 QTS000015 exon brain_hypothalamus GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000187/QTD000187.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_hypothalamus.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_hypothalamus.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_hypothalamus/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.brain_hypothalamus.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_hypothalamus/QTS000015/normalised/exon/per_million_normalised/GTEx.brain_hypothalamus.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000187_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000187_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_hypothalamus/QTS000015/normalised/ge/per_million_normalised/GTEx.brain_hypothalamus.scaling_factors.tsv.gz +QTD000192 QTS000015 exon brain_nucleus_accumbens GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000192/QTD000192.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_nucleus_accumbens.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_nucleus_accumbens.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_nucleus_accumbens/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.brain_nucleus_accumbens.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_nucleus_accumbens/QTS000015/normalised/exon/per_million_normalised/GTEx.brain_nucleus_accumbens.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000192_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000192_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_nucleus_accumbens/QTS000015/normalised/ge/per_million_normalised/GTEx.brain_nucleus_accumbens.scaling_factors.tsv.gz +QTD000197 QTS000015 exon brain_putamen GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000197/QTD000197.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_putamen.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_putamen.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_putamen/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.brain_putamen.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_putamen/QTS000015/normalised/exon/per_million_normalised/GTEx.brain_putamen.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000197_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000197_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_putamen/QTS000015/normalised/ge/per_million_normalised/GTEx.brain_putamen.scaling_factors.tsv.gz +QTD000202 QTS000015 exon brain_spinal_cord GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000202/QTD000202.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_spinal_cord.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_spinal_cord.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_spinal_cord/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.brain_spinal_cord.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_spinal_cord/QTS000015/normalised/exon/per_million_normalised/GTEx.brain_spinal_cord.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000202_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000202_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_spinal_cord/QTS000015/normalised/ge/per_million_normalised/GTEx.brain_spinal_cord.scaling_factors.tsv.gz +QTD000207 QTS000015 exon brain_substantia_nigra GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000207/QTD000207.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_substantia_nigra.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_substantia_nigra.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_substantia_nigra/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.brain_substantia_nigra.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_substantia_nigra/QTS000015/normalised/exon/per_million_normalised/GTEx.brain_substantia_nigra.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000207_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000207_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_substantia_nigra/QTS000015/normalised/ge/per_million_normalised/GTEx.brain_substantia_nigra.scaling_factors.tsv.gz +QTD000212 QTS000015 exon breast GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000212/QTD000212.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_breast.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/breast.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/breast/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.breast.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/breast/QTS000015/normalised/exon/per_million_normalised/GTEx.breast.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000212_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000212_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/breast/QTS000015/normalised/ge/per_million_normalised/GTEx.breast.scaling_factors.tsv.gz +QTD000217 QTS000015 exon fibroblast GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000217/QTD000217.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_fibroblast.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/fibroblast.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/fibroblast/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.fibroblast.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/fibroblast/QTS000015/normalised/exon/per_million_normalised/GTEx.fibroblast.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000217_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000217_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/fibroblast/QTS000015/normalised/ge/per_million_normalised/GTEx.fibroblast.scaling_factors.tsv.gz +QTD000222 QTS000015 exon LCL GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000222/QTD000222.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_LCL.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/LCL.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/LCL/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.LCL.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/LCL/QTS000015/normalised/exon/per_million_normalised/GTEx.LCL.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000222_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000222_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/LCL/QTS000015/normalised/ge/per_million_normalised/GTEx.LCL.scaling_factors.tsv.gz +QTD000227 QTS000015 exon colon_sigmoid GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000227/QTD000227.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_colon_sigmoid.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/colon_sigmoid.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/colon_sigmoid/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.colon_sigmoid.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/colon_sigmoid/QTS000015/normalised/exon/per_million_normalised/GTEx.colon_sigmoid.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000227_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000227_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/colon_sigmoid/QTS000015/normalised/ge/per_million_normalised/GTEx.colon_sigmoid.scaling_factors.tsv.gz +QTD000237 QTS000015 exon esophagus_gej GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000237/QTD000237.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_esophagus_gej.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/esophagus_gej.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/esophagus_gej/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.esophagus_gej.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/esophagus_gej/QTS000015/normalised/exon/per_million_normalised/GTEx.esophagus_gej.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000237_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000237_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/esophagus_gej/QTS000015/normalised/ge/per_million_normalised/GTEx.esophagus_gej.scaling_factors.tsv.gz +QTD000242 QTS000015 exon esophagus_mucosa GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000242/QTD000242.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_esophagus_mucosa.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/esophagus_mucosa.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/esophagus_mucosa/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.esophagus_mucosa.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/esophagus_mucosa/QTS000015/normalised/exon/per_million_normalised/GTEx.esophagus_mucosa.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000242_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000242_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/esophagus_mucosa/QTS000015/normalised/ge/per_million_normalised/GTEx.esophagus_mucosa.scaling_factors.tsv.gz +QTD000247 QTS000015 exon esophagus_muscularis GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000247/QTD000247.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_esophagus_muscularis.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/esophagus_muscularis.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/esophagus_muscularis/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.esophagus_muscularis.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/esophagus_muscularis/QTS000015/normalised/exon/per_million_normalised/GTEx.esophagus_muscularis.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000247_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000247_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/esophagus_muscularis/QTS000015/normalised/ge/per_million_normalised/GTEx.esophagus_muscularis.scaling_factors.tsv.gz +QTD000252 QTS000015 exon heart_atrial_appendage GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000252/QTD000252.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_heart_atrial_appendage.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/heart_atrial_appendage.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/heart_atrial_appendage/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.heart_atrial_appendage.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/heart_atrial_appendage/QTS000015/normalised/exon/per_million_normalised/GTEx.heart_atrial_appendage.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000252_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000252_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/heart_atrial_appendage/QTS000015/normalised/ge/per_million_normalised/GTEx.heart_atrial_appendage.scaling_factors.tsv.gz +QTD000257 QTS000015 exon heart_left_ventricle GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000257/QTD000257.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_heart_left_ventricle.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/heart_left_ventricle.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/heart_left_ventricle/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.heart_left_ventricle.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/heart_left_ventricle/QTS000015/normalised/exon/per_million_normalised/GTEx.heart_left_ventricle.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000257_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000257_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/heart_left_ventricle/QTS000015/normalised/ge/per_million_normalised/GTEx.heart_left_ventricle.scaling_factors.tsv.gz +QTD000262 QTS000015 exon kidney_cortex GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000262/QTD000262.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_kidney_cortex.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/kidney_cortex.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/kidney_cortex/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.kidney_cortex.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/kidney_cortex/QTS000015/normalised/exon/per_million_normalised/GTEx.kidney_cortex.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000262_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000262_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/kidney_cortex/QTS000015/normalised/ge/per_million_normalised/GTEx.kidney_cortex.scaling_factors.tsv.gz +QTD000267 QTS000015 exon liver GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000267/QTD000267.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_liver.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/liver.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/liver/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.liver.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/liver/QTS000015/normalised/exon/per_million_normalised/GTEx.liver.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000267_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000267_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/liver/QTS000015/normalised/ge/per_million_normalised/GTEx.liver.scaling_factors.tsv.gz +QTD000272 QTS000015 exon lung GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000272/QTD000272.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_lung.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/lung.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/lung/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.lung.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/lung/QTS000015/normalised/exon/per_million_normalised/GTEx.lung.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000272_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000272_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/lung/QTS000015/normalised/ge/per_million_normalised/GTEx.lung.scaling_factors.tsv.gz +QTD000277 QTS000015 exon minor_salivary_gland GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000277/QTD000277.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_minor_salivary_gland.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/minor_salivary_gland.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/minor_salivary_gland/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.minor_salivary_gland.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/minor_salivary_gland/QTS000015/normalised/exon/per_million_normalised/GTEx.minor_salivary_gland.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000277_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000277_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz 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/gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000282_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/muscle/QTS000015/normalised/ge/per_million_normalised/GTEx.muscle.scaling_factors.tsv.gz +QTD000287 QTS000015 exon nerve_tibial GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000287/QTD000287.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_nerve_tibial.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/nerve_tibial.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/nerve_tibial/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.nerve_tibial.tsv.gz 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/gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/ovary.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/ovary/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.ovary.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/ovary/QTS000015/normalised/exon/per_million_normalised/GTEx.ovary.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000292_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000292_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/ovary/QTS000015/normalised/ge/per_million_normalised/GTEx.ovary.scaling_factors.tsv.gz +QTD000297 QTS000015 exon pancreas GTEx 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/gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/pancreas/QTS000015/normalised/ge/per_million_normalised/GTEx.pancreas.scaling_factors.tsv.gz +QTD000302 QTS000015 exon pituitary GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000302/QTD000302.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_pituitary.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/pituitary.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/pituitary/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.pituitary.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/pituitary/QTS000015/normalised/exon/per_million_normalised/GTEx.pituitary.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000302_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000302_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/pituitary/QTS000015/normalised/ge/per_million_normalised/GTEx.pituitary.scaling_factors.tsv.gz +QTD000307 QTS000015 exon prostate GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000307/QTD000307.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_prostate.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/prostate.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/prostate/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.prostate.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/prostate/QTS000015/normalised/exon/per_million_normalised/GTEx.prostate.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000307_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000307_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/prostate/QTS000015/normalised/ge/per_million_normalised/GTEx.prostate.scaling_factors.tsv.gz +QTD000312 QTS000015 exon skin_not_sun_exposed GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000312/QTD000312.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_skin_not_sun_exposed.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/skin_not_sun_exposed.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/skin_not_sun_exposed/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.skin_not_sun_exposed.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/skin_not_sun_exposed/QTS000015/normalised/exon/per_million_normalised/GTEx.skin_not_sun_exposed.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000312_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000312_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/skin_not_sun_exposed/QTS000015/normalised/ge/per_million_normalised/GTEx.skin_not_sun_exposed.scaling_factors.tsv.gz +QTD000317 QTS000015 exon skin_sun_exposed GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000317/QTD000317.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_skin_sun_exposed.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/skin_sun_exposed.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/skin_sun_exposed/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.skin_sun_exposed.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/skin_sun_exposed/QTS000015/normalised/exon/per_million_normalised/GTEx.skin_sun_exposed.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000317_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000317_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/skin_sun_exposed/QTS000015/normalised/ge/per_million_normalised/GTEx.skin_sun_exposed.scaling_factors.tsv.gz +QTD000322 QTS000015 exon small_intestine GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000322/QTD000322.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_small_intestine.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/small_intestine.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/small_intestine/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.small_intestine.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/small_intestine/QTS000015/normalised/exon/per_million_normalised/GTEx.small_intestine.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000322_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000322_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/small_intestine/QTS000015/normalised/ge/per_million_normalised/GTEx.small_intestine.scaling_factors.tsv.gz +QTD000327 QTS000015 exon spleen GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000327/QTD000327.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_spleen.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/spleen.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/spleen/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.spleen.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/spleen/QTS000015/normalised/exon/per_million_normalised/GTEx.spleen.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000327_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000327_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/spleen/QTS000015/normalised/ge/per_million_normalised/GTEx.spleen.scaling_factors.tsv.gz +QTD000332 QTS000015 exon stomach GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000332/QTD000332.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_stomach.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/stomach.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/stomach/QTS000015/normalised/exon/qtl_group_split_norm/GTEx.stomach.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/stomach/QTS000015/normalised/exon/per_million_normalised/GTEx.stomach.exon_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000332_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000332_sumstats_copy.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/stomach/QTS000015/normalised/ge/per_million_normalised/GTEx.stomach.scaling_factors.tsv.gz +QTD000337 QTS000015 exon testis GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000337/QTD000337.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_testis.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/testis.parquet 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/gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000256_sumstats.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/gene_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/heart_left_ventricle/QTS000015/normalised/ge/per_million_normalised/GTEx.heart_left_ventricle.scaling_factors.tsv.gz +QTD000231 QTS000015 ge colon_transverse GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000231/QTD000231.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_colon_transverse.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/colon_transverse.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/colon_transverse/QTS000015/normalised/ge/qtl_group_split_norm/GTEx.colon_transverse.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/colon_transverse/QTS000015/normalised/ge/per_million_normalised/GTEx.colon_transverse.gene_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000232_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000231_sumstats.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/gene_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/colon_transverse/QTS000015/normalised/ge/per_million_normalised/GTEx.colon_transverse.scaling_factors.tsv.gz \ No newline at end of file diff --git a/input/GTEx_V10_all/GTEx_V10_input_ge_blood.tsv b/input/GTEx_V10_all/GTEx_V10_input_ge_blood.tsv new file mode 100644 index 0000000..cf7262f --- /dev/null +++ b/input/GTEx_V10_all/GTEx_V10_input_ge_blood.tsv @@ -0,0 +1,2 @@ +dataset_id study_id quant_method qtl_group study_name credible_sets_file sample_meta vcf_file coverage_path usage_matrix_norm tpm_matrix exon_summ_stats_files all_summ_stats_files pheno_meta scaling_factors +QTD000356 QTS000015 ge blood GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000356/QTD000356.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_blood.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/blood.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/blood/QTS000015/normalised/ge/qtl_group_split_norm/GTEx.blood.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/blood/QTS000015/normalised/ge/per_million_normalised/GTEx.blood.gene_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000357_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000356_sumstats.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/gene_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/blood/QTS000015/normalised/ge/per_million_normalised/GTEx.blood.scaling_factors.tsv.gz diff --git a/input/GTEx_V10_all/GTEx_V10_input_ge_colon_transverse.tsv b/input/GTEx_V10_all/GTEx_V10_input_ge_colon_transverse.tsv new file mode 100644 index 0000000..cd80fc6 --- /dev/null +++ b/input/GTEx_V10_all/GTEx_V10_input_ge_colon_transverse.tsv @@ -0,0 +1,2 @@ +dataset_id study_id quant_method qtl_group study_name credible_sets_file sample_meta vcf_file coverage_path usage_matrix_norm tpm_matrix exon_summ_stats_files all_summ_stats_files pheno_meta scaling_factors +QTD000231 QTS000015 ge colon_transverse GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000231/QTD000231.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_colon_transverse.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/colon_transverse_10122025.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/colon_transverse/QTS000015/normalised/ge/qtl_group_split_norm/GTEx.colon_transverse.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/colon_transverse/QTS000015/normalised/ge/per_million_normalised/GTEx.colon_transverse.gene_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000232_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000231_sumstats.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/gene_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/colon_transverse/QTS000015/normalised/ge/per_million_normalised/GTEx.colon_transverse.scaling_factors.tsv.gz diff --git a/input/GTEx_V10_all/GTEx_V10_input_ge_completed.tsv b/input/GTEx_V10_all/GTEx_V10_input_ge_completed.tsv new file mode 100644 index 0000000..6cf229f --- /dev/null +++ b/input/GTEx_V10_all/GTEx_V10_input_ge_completed.tsv @@ -0,0 +1,2 @@ +dataset_id study_id quant_method qtl_group study_name credible_sets_file sample_meta vcf_file coverage_path usage_matrix_norm tpm_matrix exon_summ_stats_files all_summ_stats_files pheno_meta scaling_factors +QTD000316 QTS000015 ge skin_sun_exposed GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000316/QTD000316.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_skin_sun_exposed.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/skin_sun_exposed.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/skin_sun_exposed/QTS000015/normalised/ge/qtl_group_split_norm/GTEx.skin_sun_exposed.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/skin_sun_exposed/QTS000015/normalised/ge/per_million_normalised/GTEx.skin_sun_exposed.gene_counts_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000317_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000316_sumstats.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/gene_counts_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/skin_sun_exposed/QTS000015/normalised/ge/per_million_normalised/GTEx.skin_sun_exposed.scaling_factors.tsv.gz \ No newline at end of file diff --git a/input/GTEx_V10_all/GTEx_V10_inputs_leafcutter_all.tsv b/input/GTEx_V10_all/GTEx_V10_inputs_leafcutter_all.tsv new file mode 100644 index 0000000..a73a766 --- /dev/null +++ b/input/GTEx_V10_all/GTEx_V10_inputs_leafcutter_all.tsv @@ -0,0 +1,46 @@ +dataset_id study_id quant_method qtl_group study_name credible_sets_file sample_meta vcf_file coverage_path usage_matrix_norm tpm_matrix exon_summ_stats_files all_summ_stats_files pheno_meta scaling_factors +QTD000120 QTS000015 leafcutter adipose_subcutaneous GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000120/QTD000120.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_adipose_subcutaneous.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/adipose_subcutaneous.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/leafcutter/qtl_group_split_norm/GTEx.adipose_subcutaneous.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/leafcutter/per_million_normalised/GTEx.adipose_subcutaneous.leafcutter_CPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000117_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000120_sumstats.tsv /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/leafcutter/leafcutter_metadata.txt.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/ge/per_million_normalised/GTEx.adipose_subcutaneous.scaling_factors.tsv.gz +QTD000125 QTS000015 leafcutter adipose_visceral GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000125/QTD000125.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_adipose_visceral.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/adipose_visceral.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_visceral/QTS000015/normalised/leafcutter/qtl_group_split_norm/GTEx.adipose_visceral.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_visceral/QTS000015/normalised/leafcutter/per_million_normalised/GTEx.adipose_visceral.leafcutter_CPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000122_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000125_sumstats.tsv /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_visceral/QTS000015/normalised/leafcutter/leafcutter_metadata.txt.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_visceral/QTS000015/normalised/ge/per_million_normalised/GTEx.adipose_visceral.scaling_factors.tsv.gz +QTD000135 QTS000015 leafcutter artery_aorta GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000135/QTD000135.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_artery_aorta.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/artery_aorta.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_aorta/QTS000015/normalised/leafcutter/qtl_group_split_norm/GTEx.artery_aorta.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_aorta/QTS000015/normalised/leafcutter/per_million_normalised/GTEx.artery_aorta.leafcutter_CPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000132_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000135_sumstats.tsv /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_aorta/QTS000015/normalised/leafcutter/leafcutter_metadata.txt.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_aorta/QTS000015/normalised/ge/per_million_normalised/GTEx.artery_aorta.scaling_factors.tsv.gz +QTD000140 QTS000015 leafcutter artery_coronary GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000140/QTD000140.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_artery_coronary.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/artery_coronary.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_coronary/QTS000015/normalised/leafcutter/qtl_group_split_norm/GTEx.artery_coronary.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_coronary/QTS000015/normalised/leafcutter/per_million_normalised/GTEx.artery_coronary.leafcutter_CPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000137_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000140_sumstats.tsv 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/gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_tibial/QTS000015/normalised/leafcutter/per_million_normalised/GTEx.artery_tibial.leafcutter_CPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000142_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000145_sumstats.tsv /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_tibial/QTS000015/normalised/leafcutter/leafcutter_metadata.txt.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_tibial/QTS000015/normalised/ge/per_million_normalised/GTEx.artery_tibial.scaling_factors.tsv.gz +QTD000150 QTS000015 leafcutter brain_amygdala GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000150/QTD000150.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_amygdala.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_amygdala.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_amygdala/QTS000015/normalised/leafcutter/qtl_group_split_norm/GTEx.brain_amygdala.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_amygdala/QTS000015/normalised/leafcutter/per_million_normalised/GTEx.brain_amygdala.leafcutter_CPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000147_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000150_sumstats.tsv /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_amygdala/QTS000015/normalised/leafcutter/leafcutter_metadata.txt.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_amygdala/QTS000015/normalised/ge/per_million_normalised/GTEx.brain_amygdala.scaling_factors.tsv.gz 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/gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/skin_sun_exposed/QTS000015/normalised/ge/per_million_normalised/GTEx.skin_sun_exposed.scaling_factors.tsv.gz diff --git a/input/GTEx_V10_all/GTEx_V10_inputs_leafcutter_corrupted.tsv b/input/GTEx_V10_all/GTEx_V10_inputs_leafcutter_corrupted.tsv new file mode 100644 index 0000000..b3ee3ed --- /dev/null +++ b/input/GTEx_V10_all/GTEx_V10_inputs_leafcutter_corrupted.tsv @@ -0,0 +1,4 @@ +dataset_id study_id quant_method qtl_group study_name credible_sets_file sample_meta vcf_file coverage_path usage_matrix_norm tpm_matrix exon_summ_stats_files all_summ_stats_files pheno_meta scaling_factors +QTD000130 QTS000015 leafcutter adrenal_gland GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000130/QTD000130.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_adrenal_gland.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz 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/gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/colon_transverse/QTS000015/normalised/leafcutter/leafcutter_metadata.txt.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/colon_transverse/QTS000015/normalised/ge/per_million_normalised/GTEx.colon_transverse.scaling_factors.tsv.gz +QTD000350 QTS000015 leafcutter uterus GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000350/QTD000350.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_uterus.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/uterus.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/uterus/QTS000015/normalised/leafcutter/qtl_group_split_norm/GTEx.uterus.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/uterus/QTS000015/normalised/leafcutter/per_million_normalised/GTEx.uterus.leafcutter_CPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000347_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000350_sumstats.tsv /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/uterus/QTS000015/normalised/leafcutter/leafcutter_metadata.txt.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/uterus/QTS000015/normalised/ge/per_million_normalised/GTEx.uterus.scaling_factors.tsv.gz diff --git a/input/GTEx_V10_all/GTEx_V10_inputs_tx_all.tsv b/input/GTEx_V10_all/GTEx_V10_inputs_tx_all.tsv new file mode 100644 index 0000000..f13cfaa --- /dev/null +++ b/input/GTEx_V10_all/GTEx_V10_inputs_tx_all.tsv @@ -0,0 +1,49 @@ +dataset_id study_id quant_method qtl_group study_name credible_sets_file sample_meta vcf_file coverage_path usage_matrix_norm tpm_matrix exon_summ_stats_files all_summ_stats_files pheno_meta scaling_factors +QTD000118 QTS000015 tx adipose_subcutaneous GTEx 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/gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/transcript_usage_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_subcutaneous/QTS000015/normalised/ge/per_million_normalised/GTEx.adipose_subcutaneous.scaling_factors.tsv.gz +QTD000123 QTS000015 tx adipose_visceral GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000123/QTD000123.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_adipose_visceral.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/adipose_visceral.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adipose_visceral/QTS000015/normalised/tx/qtl_group_split_norm/GTEx.adipose_visceral.tsv.gz 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/gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/adrenal_gland.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adrenal_gland/QTS000015/normalised/tx/qtl_group_split_norm/GTEx.adrenal_gland.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adrenal_gland/QTS000015/normalised/tx/per_million_normalised/GTEx.adrenal_gland.transcript_usage_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000127_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000128_sumstats.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/transcript_usage_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/adrenal_gland/QTS000015/normalised/ge/per_million_normalised/GTEx.adrenal_gland.scaling_factors.tsv.gz 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/gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/transcript_usage_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_aorta/QTS000015/normalised/ge/per_million_normalised/GTEx.artery_aorta.scaling_factors.tsv.gz +QTD000138 QTS000015 tx artery_coronary GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000138/QTD000138.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_artery_coronary.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/artery_coronary.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_coronary/QTS000015/normalised/tx/qtl_group_split_norm/GTEx.artery_coronary.tsv.gz 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/gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/artery_tibial.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_tibial/QTS000015/normalised/tx/qtl_group_split_norm/GTEx.artery_tibial.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_tibial/QTS000015/normalised/tx/per_million_normalised/GTEx.artery_tibial.transcript_usage_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000142_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000143_sumstats.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/transcript_usage_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/artery_tibial/QTS000015/normalised/ge/per_million_normalised/GTEx.artery_tibial.scaling_factors.tsv.gz +QTD000148 QTS000015 tx brain_amygdala GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000148/QTD000148.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_amygdala.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_amygdala.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_amygdala/QTS000015/normalised/tx/qtl_group_split_norm/GTEx.brain_amygdala.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_amygdala/QTS000015/normalised/tx/per_million_normalised/GTEx.brain_amygdala.transcript_usage_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000147_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000148_sumstats.tsv 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/gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_caudate.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_caudate.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_caudate/QTS000015/normalised/tx/qtl_group_split_norm/GTEx.brain_caudate.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_caudate/QTS000015/normalised/tx/per_million_normalised/GTEx.brain_caudate.transcript_usage_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000157_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000158_sumstats.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/transcript_usage_Ensembl_105_phenotype_metadata.tsv.gz 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/gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000162_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000163_sumstats.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/transcript_usage_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_cerebellar_hemisphere/QTS000015/normalised/ge/per_million_normalised/GTEx.brain_cerebellar_hemisphere.scaling_factors.tsv.gz +QTD000168 QTS000015 tx brain_cerebellum GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000168/QTD000168.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_cerebellum.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_cerebellum.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_cerebellum/QTS000015/normalised/tx/qtl_group_split_norm/GTEx.brain_cerebellum.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_cerebellum/QTS000015/normalised/tx/per_million_normalised/GTEx.brain_cerebellum.transcript_usage_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000167_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000168_sumstats.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/transcript_usage_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_cerebellum/QTS000015/normalised/ge/per_million_normalised/GTEx.brain_cerebellum.scaling_factors.tsv.gz +QTD000173 QTS000015 tx brain_cortex GTEx 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/gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_hippocampus.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_hippocampus.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_hippocampus/QTS000015/normalised/tx/qtl_group_split_norm/GTEx.brain_hippocampus.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_hippocampus/QTS000015/normalised/tx/per_million_normalised/GTEx.brain_hippocampus.transcript_usage_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000182_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000183_sumstats.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/transcript_usage_Ensembl_105_phenotype_metadata.tsv.gz 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/gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000187_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000188_sumstats.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/transcript_usage_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_hypothalamus/QTS000015/normalised/ge/per_million_normalised/GTEx.brain_hypothalamus.scaling_factors.tsv.gz +QTD000193 QTS000015 tx brain_nucleus_accumbens GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000193/QTD000193.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_nucleus_accumbens.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_nucleus_accumbens.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_nucleus_accumbens/QTS000015/normalised/tx/qtl_group_split_norm/GTEx.brain_nucleus_accumbens.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_nucleus_accumbens/QTS000015/normalised/tx/per_million_normalised/GTEx.brain_nucleus_accumbens.transcript_usage_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000192_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000193_sumstats.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/transcript_usage_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_nucleus_accumbens/QTS000015/normalised/ge/per_million_normalised/GTEx.brain_nucleus_accumbens.scaling_factors.tsv.gz 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/gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_substantia_nigra.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/brain_substantia_nigra.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_substantia_nigra/QTS000015/normalised/tx/qtl_group_split_norm/GTEx.brain_substantia_nigra.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/brain_substantia_nigra/QTS000015/normalised/tx/per_million_normalised/GTEx.brain_substantia_nigra.transcript_usage_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000207_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000208_sumstats.tsv 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/gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/esophagus_gej.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/esophagus_gej/QTS000015/normalised/tx/qtl_group_split_norm/GTEx.esophagus_gej.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/esophagus_gej/QTS000015/normalised/tx/per_million_normalised/GTEx.esophagus_gej.transcript_usage_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000237_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000238_sumstats.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/transcript_usage_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/esophagus_gej/QTS000015/normalised/ge/per_million_normalised/GTEx.esophagus_gej.scaling_factors.tsv.gz 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/gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_heart_atrial_appendage.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/heart_atrial_appendage.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/heart_atrial_appendage/QTS000015/normalised/tx/qtl_group_split_norm/GTEx.heart_atrial_appendage.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/heart_atrial_appendage/QTS000015/normalised/tx/per_million_normalised/GTEx.heart_atrial_appendage.transcript_usage_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000252_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000253_sumstats.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/transcript_usage_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/heart_atrial_appendage/QTS000015/normalised/ge/per_million_normalised/GTEx.heart_atrial_appendage.scaling_factors.tsv.gz +QTD000258 QTS000015 tx heart_left_ventricle GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000258/QTD000258.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_heart_left_ventricle.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/heart_left_ventricle.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/heart_left_ventricle/QTS000015/normalised/tx/qtl_group_split_norm/GTEx.heart_left_ventricle.tsv.gz 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/gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_kidney_cortex.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/kidney_cortex.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/kidney_cortex/QTS000015/normalised/tx/qtl_group_split_norm/GTEx.kidney_cortex.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/kidney_cortex/QTS000015/normalised/tx/per_million_normalised/GTEx.kidney_cortex.transcript_usage_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000262_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000263_sumstats.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/transcript_usage_Ensembl_105_phenotype_metadata.tsv.gz 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/gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000268_sumstats.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/transcript_usage_Ensembl_105_phenotype_metadata.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/liver/QTS000015/normalised/ge/per_million_normalised/GTEx.liver.scaling_factors.tsv.gz +QTD000273 QTS000015 tx lung GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000273/QTD000273.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_lung.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/lung.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/lung/QTS000015/normalised/tx/qtl_group_split_norm/GTEx.lung.tsv.gz 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/gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/minor_salivary_gland.parquet /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/minor_salivary_gland/QTS000015/normalised/tx/qtl_group_split_norm/GTEx.minor_salivary_gland.tsv.gz /gpfs/helios/projects/eQTLCatalogue/qcnorm2/QTS000015/minor_salivary_gland/QTS000015/normalised/tx/per_million_normalised/GTEx.minor_salivary_gland.transcript_usage_TPM_norm.tsv.gz /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000277_sumstats.tsv /gpfs/helios/home/kerimov/alasoo_lab/eqtl_plot_data_generator/input/GTEx_V10_all/sumstats_files/QTD000278_sumstats.tsv /gpfs/space/projects/genomic_references/annotations/eQTLCatalogue/v1.0/phenotype_metadata/transcript_usage_Ensembl_105_phenotype_metadata.tsv.gz 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a/input/GTEx_V10_all/GTEx_V10_inputs_tx_corrupted.tsv b/input/GTEx_V10_all/GTEx_V10_inputs_tx_corrupted.tsv new file mode 100644 index 0000000..86b08ea --- /dev/null +++ b/input/GTEx_V10_all/GTEx_V10_inputs_tx_corrupted.tsv @@ -0,0 +1,2 @@ +dataset_id study_id quant_method qtl_group study_name credible_sets_file sample_meta vcf_file coverage_path usage_matrix_norm tpm_matrix exon_summ_stats_files all_summ_stats_files pheno_meta scaling_factors +QTD000233 QTS000015 tx colon_transverse GTEx /gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/susie/QTS000015/QTD000233/QTD000233.credible_sets.parquet /gpfs/helios/home/kerimov/alasoo_lab/SampleArcheology/studies/GTEx/v10_metadata/GTExV10_metadata_colon_transverse.tsv /gpfs/helios/projects/GTEx/genotypes/GTEx_v10/GTEx_v9.MAF001.vcf.gz /gpfs/helios/projects/eQTLCatalogue/coverage_parquet/GTEx_v10/colon_transverse.parquet 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+/gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/exon_sumstats/QTS000015/QTD000360/all/QTD000360_chr_X_153435598_157024758.parquet +/gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/exon_sumstats/QTS000015/QTD000360/all/QTD000360_chr_X_1908178_15025645.parquet +/gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/exon_sumstats/QTS000015/QTD000360/all/QTD000360_chr_X_20972190_41642232.parquet +/gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/exon_sumstats/QTS000015/QTD000360/all/QTD000360_chr_X_39642232_48236146.parquet +/gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/exon_sumstats/QTS000015/QTD000360/all/QTD000360_chr_X_46236146_49950630.parquet +/gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/exon_sumstats/QTS000015/QTD000360/all/QTD000360_chr_X_47950630_54222829.parquet +/gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/exon_sumstats/QTS000015/QTD000360/all/QTD000360_chr_X_52222829_58117437.parquet +/gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/exon_sumstats/QTS000015/QTD000360/all/QTD000360_chr_X_56117437_72129946.parquet +/gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/exon_sumstats/QTS000015/QTD000360/all/QTD000360_chr_X_70133964_78751614.parquet +/gpfs/helios/projects/eQTLCatalogue/qtlmap/eQTL_Catalogue_r8/exon_sumstats/QTS000015/QTD000360/all/QTD000360_chr_X_76751614_102658951.parquet diff --git a/main.nf b/main.nf index 987a7ba..07e4600 100644 --- a/main.nf +++ b/main.nf @@ -15,7 +15,7 @@ if( !(workflow.runName ==~ /[a-z]+_[a-z]+/) ){ Channel.fromPath(params.studyFile) .ifEmpty { error "Cannot find studyFile file in: ${params.studyFile}" } .splitCsv(header: true, sep: '\t', strip: true) - .map{row -> [ row.dataset_id, row.study_id, row.quant_method, row.qtl_group, row.study_name, file(row.credible_sets_file), file(row.sample_meta), file(row.bigwig_path), file(row.usage_matrix_norm), file(row.tpm_matrix), file(row.exon_summ_stats_files), file(row.all_summ_stats_files), file(row.pheno_meta), file(row.scaling_factors) ]} + .map{row -> [ row.dataset_id, row.study_id, row.quant_method, row.qtl_group, row.study_name, file(row.credible_sets_file), file(row.sample_meta), file(row.coverage_path), file(row.usage_matrix_norm), file(row.tpm_matrix), file(row.exon_summ_stats_files), file(row.all_summ_stats_files), file(row.pheno_meta), file(row.scaling_factors) ]} .branch { ge: it[2] == "ge" exon: it[2] == "exon" diff --git a/modules/generate_plot_data.nf b/modules/generate_plot_data.nf index 5119712..dd72d71 100644 --- a/modules/generate_plot_data.nf +++ b/modules/generate_plot_data.nf @@ -2,11 +2,11 @@ process generate_plot_ge_data { tag "${dataset_id}_${qtl_group}_${quant_method}" label "generate_plot_data" - container "quay.io/kfkf33/coverage_plot:v3" + container "quay.io/kerimoff/coverage_plot:v6" input: - tuple val(dataset_id), val(quant_method), val(qtl_group), file(sample_meta), file(bigwig_path), file(usage_matrix_norm), file(tpm_matrix), file(exon_summ_stats_files), file(all_summ_stats_files), file(phenotype_meta), file(scaling_factors), file(vcf_file), file(vcf_file_index), file(susie_purity_filtered) + tuple val(dataset_id), val(quant_method), val(qtl_group), file(sample_meta), file(coverage_parquet), file(usage_matrix_norm), file(tpm_matrix), file(exon_summ_stats_files), file(all_summ_stats_files), file(phenotype_meta), file(scaling_factors), file(vcf_file), file(vcf_file_index), file(susie_purity_filtered) path mane_transcript_gene_map path mane_gtf_file @@ -24,7 +24,7 @@ process generate_plot_ge_data { --finemap_susie $susie_purity_filtered \ --sample_meta $sample_meta \ --vcf_file $vcf_file \ - --bigwig_path $bigwig_path \ + --coverage_parquet $coverage_parquet \ --mane_transcript_gene_map $mane_transcript_gene_map \ --gtf_file $mane_gtf_file \ --div_scaling_factors $scaling_factors \ @@ -39,11 +39,11 @@ process generate_plot_ge_data { process generate_plot_exon_data { tag "${dataset_id}_${qtl_group}_${quant_method}" label "generate_plot_data" - container "quay.io/kfkf33/coverage_plot:v3" + container "quay.io/kerimoff/coverage_plot:v6" input: - tuple val(dataset_id), val(quant_method), val(qtl_group), file(sample_meta), file(bigwig_path), file(usage_matrix_norm), file(tpm_matrix), file(exon_summ_stats_files), file(all_summ_stats_files), file(phenotype_meta), file(scaling_factors), file(vcf_file), file(vcf_file_index), file(susie_purity_filtered) + tuple val(dataset_id), val(quant_method), val(qtl_group), file(sample_meta), file(coverage_parquet), file(usage_matrix_norm), file(tpm_matrix), file(exon_summ_stats_files), file(all_summ_stats_files), file(phenotype_meta), file(scaling_factors), file(vcf_file), file(vcf_file_index), file(susie_purity_filtered) path mane_transcript_gene_map path mane_gtf_file @@ -62,7 +62,7 @@ process generate_plot_exon_data { --finemap_susie $susie_purity_filtered \ --sample_meta $sample_meta \ --vcf_file $vcf_file \ - --bigwig_path $bigwig_path \ + --coverage_parquet $coverage_parquet \ --mane_transcript_gene_map $mane_transcript_gene_map \ --gtf_file $mane_gtf_file \ --div_scaling_factors $scaling_factors \ @@ -76,11 +76,11 @@ process generate_plot_exon_data { process generate_plot_leafcutter_data { tag "${dataset_id}_${qtl_group}_${quant_method}" label "generate_plot_data" - container "quay.io/kfkf33/coverage_plot:v3" + container "quay.io/kerimoff/coverage_plot:v6" input: - tuple val(dataset_id), val(quant_method), val(qtl_group), file(sample_meta), file(bigwig_path), file(usage_matrix_norm), file(tpm_matrix), file(exon_summ_stats_files), file(all_summ_stats_files), file(phenotype_meta), file(scaling_factors), file(vcf_file), file(vcf_file_index), file(susie_purity_filtered) + tuple val(dataset_id), val(quant_method), val(qtl_group), file(sample_meta), file(coverage_parquet), file(usage_matrix_norm), file(tpm_matrix), file(exon_summ_stats_files), file(all_summ_stats_files), file(phenotype_meta), file(scaling_factors), file(vcf_file), file(vcf_file_index), file(susie_purity_filtered) path mane_transcript_gene_map path mane_gtf_file @@ -99,7 +99,7 @@ process generate_plot_leafcutter_data { --finemap_susie $susie_purity_filtered \ --sample_meta $sample_meta \ --vcf_file $vcf_file \ - --bigwig_path $bigwig_path \ + --coverage_parquet $coverage_parquet \ --mane_transcript_gene_map $mane_transcript_gene_map \ --gtf_file $mane_gtf_file \ --div_scaling_factors $scaling_factors \ @@ -113,11 +113,11 @@ process generate_plot_leafcutter_data { process generate_plot_tx_data { tag "${dataset_id}_${qtl_group}_${quant_method}" label "generate_plot_data" - container "quay.io/kfkf33/coverage_plot:v3" + container "quay.io/kerimoff/coverage_plot:v6" input: - tuple val(dataset_id), val(quant_method), val(qtl_group), file(sample_meta), file(bigwig_path), file(usage_matrix_norm), file(tpm_matrix), file(exon_summ_stats_files), file(all_summ_stats_files), file(phenotype_meta), file(scaling_factors), file(vcf_file), file(vcf_file_index), file(susie_purity_filtered) + tuple val(dataset_id), val(quant_method), val(qtl_group), file(sample_meta), file(coverage_parquet), file(usage_matrix_norm), file(tpm_matrix), file(exon_summ_stats_files), file(all_summ_stats_files), file(phenotype_meta), file(scaling_factors), file(vcf_file), file(vcf_file_index), file(susie_purity_filtered) path mane_transcript_gene_map path mane_gtf_file path tx_gtf_file @@ -136,7 +136,7 @@ process generate_plot_tx_data { --sample_meta $sample_meta \ --phenotype_meta $phenotype_meta \ --vcf_file $vcf_file \ - --bigwig_path $bigwig_path \ + --coverage_parquet $coverage_parquet \ --mane_transcript_gene_map $mane_transcript_gene_map \ --gtf_file $mane_gtf_file \ --div_scaling_factors $scaling_factors \ @@ -151,11 +151,11 @@ process generate_plot_tx_data { process generate_plot_txrev_data { tag "${dataset_id}_${qtl_group}_${quant_method}" label "generate_plot_data" - container "quay.io/kfkf33/coverage_plot:v3" + container "quay.io/kerimoff/coverage_plot:v6" input: - tuple val(dataset_id), val(quant_method), val(qtl_group), file(sample_meta), file(bigwig_path), file(usage_matrix_norm), file(tpm_matrix), file(exon_summ_stats_files), file(all_summ_stats_files), file(phenotype_meta), file(scaling_factors), file(vcf_file), file(vcf_file_index), file(susie_purity_filtered) + tuple val(dataset_id), val(quant_method), val(qtl_group), file(sample_meta), file(coverage_parquet), file(usage_matrix_norm), file(tpm_matrix), file(exon_summ_stats_files), file(all_summ_stats_files), file(phenotype_meta), file(scaling_factors), file(vcf_file), file(vcf_file_index), file(susie_purity_filtered) path mane_transcript_gene_map path mane_gtf_file path txrev_gtf_file @@ -176,7 +176,7 @@ process generate_plot_txrev_data { --sample_meta $sample_meta \ --phenotype_meta $phenotype_meta \ --vcf_file $vcf_file \ - --bigwig_path $bigwig_path \ + --coverage_parquet $coverage_parquet \ --mane_transcript_gene_map $mane_transcript_gene_map \ --gtf_file $mane_gtf_file \ --div_scaling_factors $scaling_factors \ diff --git a/modules/utils.nf b/modules/utils.nf index 3fdca46..6ca5aea 100644 --- a/modules/utils.nf +++ b/modules/utils.nf @@ -21,10 +21,10 @@ process prepare_batches { label "process_low" input: - tuple val(dataset_id), val(study_id), val(quant_method), val(qtl_group), val(study_name), file(susie_purity_filtered), file(sample_meta), file(bigwig_path), file(usage_matrix_norm),file(tpm_matrix), file(exon_summ_stats_files), file(all_summ_stats_files), file(phenotype_meta), file(scaling_factors), file(vcf_file), file(vcf_file_index) + tuple val(dataset_id), val(study_id), val(quant_method), val(qtl_group), val(study_name), file(susie_purity_filtered), file(sample_meta), file(coverage_parquet), file(usage_matrix_norm),file(tpm_matrix), file(exon_summ_stats_files), file(all_summ_stats_files), file(phenotype_meta), file(scaling_factors), file(vcf_file), file(vcf_file_index) output: - tuple val(dataset_id), val(quant_method), val(qtl_group), file(sample_meta), file(bigwig_path), file(usage_matrix_norm) ,file(tpm_matrix), file(exon_summ_stats_files), file(all_summ_stats_files), file(phenotype_meta), file(scaling_factors), file(vcf_file), file(vcf_file_index), emit: study_tsv_inputs_ch + tuple val(dataset_id), val(quant_method), val(qtl_group), file(sample_meta), file(coverage_parquet), file(usage_matrix_norm) ,file(tpm_matrix), file(exon_summ_stats_files), file(all_summ_stats_files), file(phenotype_meta), file(scaling_factors), file(vcf_file), file(vcf_file_index), emit: study_tsv_inputs_ch tuple val(dataset_id), val(quant_method), val(qtl_group), file("${dataset_id}_${qtl_group}_${quant_method}*.parquet"), emit: susie_batches tuple val(study_id), val(dataset_id), val(quant_method), val(qtl_group), file("${study_id}_${dataset_id}_${qtl_group}_${quant_method}.parquet"), emit: dataset_id_credible_set_tables @@ -103,11 +103,11 @@ process convert_parquet_format { container = 'quay.io/kfkf33/duckdb_sqlite_with_path:v1' input: - tuple val(dataset_id), val(study_id), val(quant_method), val(qtl_group), val(study_name), file(susie_purity_filtered), file(sample_meta), file(bigwig_path), file(usage_matrix_norm),file(tpm_matrix), file(exon_summ_stats_files), file(all_summ_stats_files), file(phenotype_meta), file(scaling_factors), file(vcf_file), file(vcf_file_index) + tuple val(dataset_id), val(study_id), val(quant_method), val(qtl_group), val(study_name), file(susie_purity_filtered), file(sample_meta), file(coverage_parquet), file(usage_matrix_norm),file(tpm_matrix), file(exon_summ_stats_files), file(all_summ_stats_files), file(phenotype_meta), file(scaling_factors), file(vcf_file), file(vcf_file_index) output: - tuple val(dataset_id), val(study_id), val(quant_method), val(qtl_group), val(study_name), file(susie_purity_filtered), file(sample_meta), file(bigwig_path), file("${usage_matrix_norm.simpleName}.parquet"),file("${usage_matrix_norm.simpleName}_TPM.parquet"), file(exon_summ_stats_files), file(all_summ_stats_files), file(phenotype_meta), file(scaling_factors), file(vcf_file), file(vcf_file_index), emit: converted_study_input + tuple val(dataset_id), val(study_id), val(quant_method), val(qtl_group), val(study_name), file(susie_purity_filtered), file(sample_meta), file(coverage_parquet), file("${usage_matrix_norm.simpleName}.parquet"),file("${usage_matrix_norm.simpleName}_TPM.parquet"), file(exon_summ_stats_files), file(all_summ_stats_files), file(phenotype_meta), file(scaling_factors), file(vcf_file), file(vcf_file_index), emit: converted_study_input script: """ diff --git a/run_test.sh b/run_test.sh index d9010f3..2a25321 100644 --- a/run_test.sh +++ b/run_test.sh @@ -13,5 +13,5 @@ module load squashfs/4.4 module load tabix nextflow run main.nf -profile tartu_hpc -resume \ - --studyFile ge/MAGE_ge_test.tsv\ - --outdir MAGE_ge_test + --studyFile test_data/GEUVADIS_test_input.tsv\ + --outdir results/test_GEUVADIS diff --git a/sbatch_runs/run_GTEx_all_tx.sh b/sbatch_runs/run_GTEx_all_tx.sh new file mode 100644 index 0000000..a95559e --- /dev/null +++ b/sbatch_runs/run_GTEx_all_tx.sh @@ -0,0 +1,19 @@ +#!/bin/bash + +#SBATCH --time=120:00:00 +#SBATCH -N 1 +#SBATCH --ntasks-per-node=1 +#SBATCH --mem=8G +#SBATCH --job-name="plot_data" + +module load any/jdk/1.8.0_265 +module load nextflow/22.04.3 +module load any/singularity/3.7.3 +module load squashfs/4.4 +module load tabix + +nextflow info + +nextflow run main.nf -profile tartu_hpc -resume \ + --studyFile input/GTEx_V10_all/GTEx_V10_inputs_tx_all.tsv\ + --outdir /gpfs/helios/projects/eQTLCatalogue/coverage_plots/GTEx_V10_all_tx diff --git a/test_data/GEUVADIS.filtered.chr22.union.relevant.vcf.gz b/test_data/GEUVADIS.filtered.chr22.union.relevant.vcf.gz new file mode 100644 index 0000000..75e59d4 Binary files /dev/null and b/test_data/GEUVADIS.filtered.chr22.union.relevant.vcf.gz differ diff --git a/test_data/GEUVADIS.filtered.chr22.union.relevant.vcf.gz.tbi b/test_data/GEUVADIS.filtered.chr22.union.relevant.vcf.gz.tbi new file mode 100644 index 0000000..fc324dc Binary files /dev/null and b/test_data/GEUVADIS.filtered.chr22.union.relevant.vcf.gz.tbi differ diff --git a/test_data/GEUVADIS.tsv b/test_data/GEUVADIS.tsv new file mode 100644 index 0000000..ec74933 --- /dev/null +++ b/test_data/GEUVADIS.tsv @@ -0,0 +1,463 @@ +sample_id genotype_id sex cell_type condition qtl_group timepoint read_length stranded paired protocol rna_qc_passed genotype_qc_passed study biosample_id population_code population_name superpopulation_code superpopulation_name +ERR188021 NA20508 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124355 TSI Tuscan EUR European +ERR188022 NA12812 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123023 CEU CEPH EUR European +ERR188023 HG00315 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124335 FIN Finnish EUR European +ERR188024 NA12749 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124828 CEU CEPH EUR European +ERR188025 HG00377 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE FALSE GEUVADIS SAME124752 FIN Finnish EUR European +ERR188026 NA20510 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124562 TSI Tuscan EUR European +ERR188027 NA07056 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124375 CEU CEPH EUR European +ERR188028 HG00155 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124588 GBR British EUR European +ERR188029 HG00355 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125125 FIN Finnish EUR European +ERR188030 NA19119 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122944 YRI Yoruba AFR African +ERR188031 HG00350 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125121 FIN Finnish EUR European +ERR188032 NA12275 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125263 CEU CEPH EUR European +ERR188033 HG00336 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123983 FIN Finnish EUR European +ERR188034 HG00273 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123419 FIN Finnish EUR European +ERR188035 HG00123 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122875 GBR British EUR European +ERR188036 HG00236 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123273 GBR British EUR European +ERR188037 NA19236 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125001 YRI Yoruba AFR African +ERR188038 HG00345 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124919 FIN Finnish EUR European +ERR188039 NA12144 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124156 CEU CEPH EUR European +ERR188040 HG00096 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123268 GBR British EUR European +ERR188041 HG00157 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124590 GBR British EUR European +ERR188042 NA19204 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122985 YRI Yoruba AFR African +ERR188043 HG00384 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123034 FIN Finnish EUR European +ERR188044 NA18498 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124058 YRI Yoruba AFR African +ERR188045 HG00321 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123796 FIN Finnish EUR European +ERR188046 HG00320 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123797 FIN Finnish EUR European +ERR188047 NA06994 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124931 CEU CEPH EUR European +ERR188048 NA12489 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125358 CEU CEPH EUR European +ERR188049 NA11931 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125096 CEU CEPH EUR European +ERR188050 NA20518 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123178 TSI Tuscan EUR European +ERR188051 NA12830 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125289 CEU CEPH EUR European +ERR188052 NA20541 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125147 TSI Tuscan EUR European +ERR188053 HG00242 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123223 GBR British EUR European +ERR188054 NA20752 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124177 TSI Tuscan EUR European +ERR188055 NA19171 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124419 YRI Yoruba AFR African +ERR188056 HG00331 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123986 FIN Finnish EUR European +ERR188057 HG00262 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123580 GBR British EUR European +ERR188058 NA12005 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125143 CEU CEPH EUR European +ERR188059 HG00125 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122869 GBR British EUR European +ERR188060 NA18517 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124883 YRI Yoruba AFR African +ERR188061 NA12761 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124466 CEU CEPH EUR European +ERR188062 NA11992 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123964 CEU CEPH EUR European +ERR188063 NA20509 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124354 TSI Tuscan EUR European +ERR188064 NA19144 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123373 YRI Yoruba AFR African +ERR188065 HG00149 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124387 GBR British EUR European +ERR188066 NA19118 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122943 YRI Yoruba AFR African +ERR188067 NA11831 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124552 CEU CEPH EUR European +ERR188068 NA20759 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125094 TSI Tuscan EUR European +ERR188069 NA19096 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123662 YRI Yoruba AFR African +ERR188070 HG00263 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123581 GBR British EUR European +ERR188071 HG00114 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125343 GBR British EUR European +ERR188072 NA19137 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125235 YRI Yoruba AFR African +ERR188073 HG00145 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124391 GBR British EUR European +ERR188074 NA19257 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123495 YRI Yoruba AFR African +ERR188075 HG00349 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124925 FIN Finnish EUR European +ERR188076 NA12006 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125145 CEU CEPH EUR European +ERR188077 NA11893 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123044 CEU CEPH EUR European +ERR188078 HG00372 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124748 FIN Finnish EUR European +ERR188079 NA20778 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124571 TSI Tuscan EUR European +ERR188080 HG00250 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123054 GBR British EUR European +ERR188081 NA12814 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123021 CEU CEPH EUR European +ERR188082 HG00110 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125339 GBR British EUR European +ERR188083 HG00285 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122836 FIN Finnish EUR European +ERR188084 HG00152 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE FALSE GEUVADIS SAME124593 GBR British EUR European +ERR188085 NA18520 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123565 YRI Yoruba AFR African +ERR188086 NA11892 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123045 CEU CEPH EUR European +ERR188087 HG00121 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122873 GBR British EUR European +ERR188088 NA20504 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124360 TSI Tuscan EUR European +ERR188089 HG00358 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125126 FIN Finnish EUR European +ERR188090 HG00186 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123647 FIN Finnish EUR European +ERR188091 HG00256 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123048 GBR British EUR European +ERR188092 NA12546 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124777 CEU CEPH EUR European +ERR188093 NA19150 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE FALSE GEUVADIS SAME124838 YRI Yoruba AFR African +ERR188094 NA20806 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125362 TSI Tuscan EUR European +ERR188095 HG00137 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123066 GBR British EUR European +ERR188096 NA18933 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123037 YRI Yoruba AFR African +ERR188097 NA18511 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124885 YRI Yoruba AFR African +ERR188098 HG00337 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123984 FIN Finnish EUR European +ERR188099 NA12843 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123541 CEU CEPH EUR European +ERR188100 NA12762 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125109 CEU CEPH EUR European +ERR188101 NA10847 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124757 CEU CEPH EUR European +ERR188102 HG00383 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123032 FIN Finnish EUR European +ERR188103 NA19184 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123859 YRI Yoruba AFR African +ERR188104 NA19146 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125080 YRI Yoruba AFR African +ERR188105 NA20768 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124372 TSI Tuscan EUR European +ERR188106 HG00247 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE FALSE GEUVADIS SAME123220 GBR British EUR European +ERR188107 NA12342 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125155 CEU CEPH EUR European +ERR188108 NA20754 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124173 TSI Tuscan EUR European +ERR188109 NA19121 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125015 YRI Yoruba AFR African +ERR188110 NA20760 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124364 TSI Tuscan EUR European +ERR188111 HG00255 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123049 GBR British EUR European +ERR188112 HG00239 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124130 GBR British EUR European +ERR188113 HG00324 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123794 FIN Finnish EUR European +ERR188114 NA20534 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124165 TSI Tuscan EUR European +ERR188115 HG00382 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123033 FIN Finnish EUR European +ERR188116 HG00151 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124592 GBR British EUR European +ERR188117 HG00268 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123574 FIN Finnish EUR European +ERR188118 HG00181 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123644 FIN Finnish EUR European +ERR188119 HG00119 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125348 GBR British EUR European +ERR188120 NA19256 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124707 YRI Yoruba AFR African +ERR188121 HG00311 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124339 FIN Finnish EUR European +ERR188122 NA11894 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123043 CEU CEPH EUR European +ERR188123 HG00313 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124337 FIN Finnish EUR European +ERR188124 HG00351 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125122 FIN Finnish EUR European +ERR188125 NA20826 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123070 TSI Tuscan EUR European +ERR188126 NA20766 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124370 TSI Tuscan EUR European +ERR188127 HG00334 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123981 FIN Finnish EUR European +ERR188128 NA19092 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123173 YRI Yoruba AFR African +ERR188129 NA19197 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125309 YRI Yoruba AFR African +ERR188130 HG00261 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123583 GBR British EUR European +ERR188131 NA19213 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125384 YRI Yoruba AFR African +ERR188132 NA20797 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123820 TSI Tuscan EUR European +ERR188133 HG00135 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE FALSE GEUVADIS SAME123068 GBR British EUR European +ERR188134 NA12827 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125077 CEU CEPH EUR European +ERR188135 NA07346 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE FALSE GEUVADIS SAME123571 CEU CEPH EUR European +ERR188136 HG00103 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125151 GBR British EUR European +ERR188137 NA20812 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125190 TSI Tuscan EUR European +ERR188138 NA20539 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124164 TSI Tuscan EUR European +ERR188139 NA18917 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123407 YRI Yoruba AFR African +ERR188140 NA12716 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123912 CEU CEPH EUR European +ERR188141 HG00343 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124923 FIN Finnish EUR European +ERR188142 NA12287 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124641 CEU CEPH EUR European +ERR188143 NA18487 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE FALSE GEUVADIS SAME124098 YRI Yoruba AFR African +ERR188144 HG00139 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123060 GBR British EUR European +ERR188145 NA20519 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123179 TSI Tuscan EUR European +ERR188146 HG00180 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123645 FIN Finnish EUR European +ERR188147 NA20804 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125224 TSI Tuscan EUR European +ERR188148 NA12282 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124640 CEU CEPH EUR European +ERR188149 HG00182 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123643 FIN Finnish EUR European +ERR188150 HG00366 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124541 FIN Finnish EUR European +ERR188151 NA18489 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124102 YRI Yoruba AFR African +ERR188152 NA12751 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123515 CEU CEPH EUR European +ERR188153 NA20765 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124367 TSI Tuscan EUR European +ERR188154 HG00251 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123053 GBR British EUR European +ERR188155 NA20790 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123815 TSI Tuscan EUR European +ERR188156 HG00335 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123982 FIN Finnish EUR European +ERR188157 NA12872 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123387 CEU CEPH EUR European +ERR188158 NA18502 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125055 YRI Yoruba AFR African +ERR188159 HG00245 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123218 GBR British EUR European +ERR188160 NA20513 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124561 TSI Tuscan EUR European +ERR188161 NA11918 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123135 CEU CEPH EUR European +ERR188162 NA18508 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124318 YRI Yoruba AFR African +ERR188163 HG00174 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124958 FIN Finnish EUR European +ERR188164 HG00159 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124586 GBR British EUR European +ERR188165 NA18510 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124886 YRI Yoruba AFR African +ERR188166 HG00108 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125161 GBR British EUR European +ERR188167 HG00106 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123948 GBR British EUR European +ERR188168 HG00346 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125264 FIN Finnish EUR European +ERR188169 HG00338 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123990 FIN Finnish EUR European +ERR188170 NA19131 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125230 YRI Yoruba AFR African +ERR188171 NA20783 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123607 TSI Tuscan EUR European +ERR188172 NA12154 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124959 CEU CEPH EUR European +ERR188173 NA20785 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123611 TSI Tuscan EUR European +ERR188174 NA19198 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124049 YRI Yoruba AFR African +ERR188175 HG00359 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE FALSE GEUVADIS SAME125127 FIN Finnish EUR European +ERR188176 NA07357 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123412 CEU CEPH EUR European +ERR188177 NA12234 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124003 CEU CEPH EUR European +ERR188178 NA19114 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122953 YRI Yoruba AFR African +ERR188179 NA20774 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124572 TSI Tuscan EUR European +ERR188180 HG00177 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124957 FIN Finnish EUR European +ERR188181 NA12413 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124055 CEU CEPH EUR European +ERR188182 NA18912 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123404 YRI Yoruba AFR African +ERR188183 NA19185 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123858 YRI Yoruba AFR African +ERR188184 NA19147 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124613 YRI Yoruba AFR African +ERR188185 HG00260 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123582 GBR British EUR European +ERR188186 HG00115 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125344 GBR British EUR European +ERR188187 HG00176 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124956 FIN Finnish EUR European +ERR188188 NA19099 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125240 YRI Yoruba AFR African +ERR188189 HG00133 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123062 GBR British EUR European +ERR188190 HG00171 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124961 FIN Finnish EUR European +ERR188191 NA20770 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124576 TSI Tuscan EUR European +ERR188192 NA20786 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123610 TSI Tuscan EUR European +ERR188193 NA19141 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124607 YRI Yoruba AFR African +ERR188194 HG00284 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122835 FIN Finnish EUR European +ERR188195 NA20792 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123817 TSI Tuscan EUR European +ERR188196 NA12717 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123911 CEU CEPH EUR European +ERR188197 HG00341 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124922 FIN Finnish EUR European +ERR188198 HG00373 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124749 FIN Finnish EUR European +ERR188199 NA20585 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122861 TSI Tuscan EUR European +ERR188200 NA18519 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124888 YRI Yoruba AFR African +ERR188201 NA20588 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122866 TSI Tuscan EUR European +ERR188202 NA06989 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124760 CEU CEPH EUR European +ERR188203 NA20542 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125150 TSI Tuscan EUR European +ERR188204 NA20524 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124016 TSI Tuscan EUR European +ERR188205 HG00310 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124338 FIN Finnish EUR European +ERR188206 HG00100 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125154 GBR British EUR European +ERR188207 NA19222 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124147 YRI Yoruba AFR African +ERR188208 NA20538 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124163 TSI Tuscan EUR European +ERR188209 NA19214 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125386 YRI Yoruba AFR African +ERR188210 NA20816 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE FALSE GEUVADIS SAME125186 TSI Tuscan EUR European +ERR188211 NA19175 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124887 YRI Yoruba AFR African +ERR188212 HG00231 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124126 GBR British EUR European +ERR188213 NA06986 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124764 CEU CEPH EUR European +ERR188214 NA18486 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124099 YRI Yoruba AFR African +ERR188215 HG00361 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124538 FIN Finnish EUR European +ERR188216 NA12873 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123388 CEU CEPH EUR European +ERR188217 NA11832 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124554 CEU CEPH EUR European +ERR188218 HG00325 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123793 FIN Finnish EUR European +ERR188219 HG00117 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125346 GBR British EUR European +ERR188220 NA12400 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123881 CEU CEPH EUR European +ERR188221 NA19113 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123838 YRI Yoruba AFR African +ERR188222 HG00265 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123579 GBR British EUR European +ERR188223 NA18908 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123560 YRI Yoruba AFR African +ERR188224 NA20528 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124012 TSI Tuscan EUR European +ERR188225 NA19152 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123017 YRI Yoruba AFR African +ERR188226 NA20532 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124171 TSI Tuscan EUR European +ERR188227 NA12874 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123389 CEU CEPH EUR European +ERR188228 NA12829 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125075 CEU CEPH EUR European +ERR188229 NA12044 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123212 CEU CEPH EUR European +ERR188230 HG00278 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123425 FIN Finnish EUR European +ERR188231 HG00097 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123267 GBR British EUR European +ERR188232 NA19160 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123758 YRI Yoruba AFR African +ERR188233 NA11993 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE FALSE GEUVADIS SAME123965 CEU CEPH EUR European +ERR188234 NA19116 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124911 YRI Yoruba AFR African +ERR188235 NA11930 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125095 CEU CEPH EUR European +ERR188236 HG00118 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125347 GBR British EUR European +ERR188237 HG00234 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124123 GBR British EUR European +ERR188238 HG00269 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123575 FIN Finnish EUR European +ERR188239 NA20520 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124019 TSI Tuscan EUR European +ERR188240 HG00306 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124159 FIN Finnish EUR European +ERR188241 HG00356 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125123 FIN Finnish EUR European +ERR188242 HG00258 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123057 GBR British EUR European +ERR188243 NA19098 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123633 YRI Yoruba AFR African +ERR188244 NA12718 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124454 CEU CEPH EUR European +ERR188245 HG00128 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122868 GBR British EUR European +ERR188246 NA11840 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125139 CEU CEPH EUR European +ERR188247 HG00104 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE FALSE GEUVADIS SAME123950 GBR British EUR European +ERR188248 HG00178 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124964 FIN Finnish EUR European +ERR188249 NA20802 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125366 TSI Tuscan EUR European +ERR188250 HG00272 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123420 FIN Finnish EUR European +ERR188251 NA20756 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124175 TSI Tuscan EUR European +ERR188252 NA20544 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125146 TSI Tuscan EUR European +ERR188253 NA20808 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122813 TSI Tuscan EUR European +ERR188254 NA20506 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124362 TSI Tuscan EUR European +ERR188255 HG00323 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123795 FIN Finnish EUR European +ERR188256 NA12777 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125252 CEU CEPH EUR European +ERR188257 HG00143 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124393 GBR British EUR European +ERR188258 NA20530 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124169 TSI Tuscan EUR European +ERR188259 NA20582 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123474 TSI Tuscan EUR European +ERR188260 HG00369 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124534 FIN Finnish EUR European +ERR188261 NA19108 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125378 YRI Yoruba AFR African +ERR188262 NA12283 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124639 CEU CEPH EUR European +ERR188263 HG00281 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122832 FIN Finnish EUR European +ERR188264 HG00274 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123422 FIN Finnish EUR European +ERR188265 NA20814 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125188 TSI Tuscan EUR European +ERR188266 HG00282 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122833 FIN Finnish EUR European +ERR188267 HG00266 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123576 FIN Finnish EUR European +ERR188268 NA19095 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123170 YRI Yoruba AFR African +ERR188269 NA18916 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123408 YRI Yoruba AFR African +ERR188270 HG00342 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124924 FIN Finnish EUR European +ERR188271 HG00246 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123219 GBR British EUR European +ERR188272 NA11881 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123209 CEU CEPH EUR European +ERR188273 NA18505 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125062 YRI Yoruba AFR African +ERR188274 HG00277 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123423 FIN Finnish EUR European +ERR188275 NA19201 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122990 YRI Yoruba AFR African +ERR188276 NA20758 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125117 TSI Tuscan EUR European +ERR188277 NA12340 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125157 CEU CEPH EUR European +ERR188278 NA18861 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124905 YRI Yoruba AFR African +ERR188279 NA12776 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124256 CEU CEPH EUR European +ERR188280 HG00381 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123030 FIN Finnish EUR European +ERR188281 NA20801 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125365 TSI Tuscan EUR European +ERR188282 NA20809 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125359 TSI Tuscan EUR European +ERR188283 NA18907 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123563 YRI Yoruba AFR African +ERR188284 NA19223 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125223 YRI Yoruba AFR African +ERR188285 HG00122 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122876 GBR British EUR European +ERR188286 NA20805 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125361 TSI Tuscan EUR European +ERR188287 HG00156 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE FALSE GEUVADIS SAME123276 GBR British EUR European +ERR188288 NA20507 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124361 TSI Tuscan EUR European +ERR188289 HG00232 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124128 GBR British EUR European +ERR188290 NA20811 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123069 TSI Tuscan EUR European +ERR188291 NA12813 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123024 CEU CEPH EUR European +ERR188292 NA19189 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123869 YRI Yoruba AFR African +ERR188293 HG00116 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125345 GBR British EUR European +ERR188294 HG00332 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123987 FIN Finnish EUR European +ERR188295 NA20757 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124176 TSI Tuscan EUR European +ERR188296 HG00330 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123985 FIN Finnish EUR European +ERR188297 NA20503 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124357 TSI Tuscan EUR European +ERR188298 NA18867 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124904 YRI Yoruba AFR African +ERR188299 HG00376 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124751 FIN Finnish EUR European +ERR188300 HG00319 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124334 FIN Finnish EUR European +ERR188301 NA11994 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123967 CEU CEPH EUR European +ERR188302 HG00183 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123642 FIN Finnish EUR European +ERR188303 HG00364 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124543 FIN Finnish EUR European +ERR188304 HG00179 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124965 FIN Finnish EUR European +ERR188305 NA20773 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124575 TSI Tuscan EUR European +ERR188306 NA19138 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125236 YRI Yoruba AFR African +ERR188307 HG00101 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125153 GBR British EUR European +ERR188308 NA12760 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124465 CEU CEPH EUR European +ERR188309 HG00150 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124591 GBR British EUR European +ERR188310 HG00124 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE FALSE GEUVADIS SAME122870 GBR British EUR European +ERR188311 NA18488 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124103 YRI Yoruba AFR African +ERR188312 HG00233 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124127 GBR British EUR European +ERR188313 NA18873 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123536 YRI Yoruba AFR African +ERR188314 HG00380 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123031 FIN Finnish EUR European +ERR188315 HG00120 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122874 GBR British EUR European +ERR188316 NA20796 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123819 TSI Tuscan EUR European +ERR188317 NA20527 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124013 TSI Tuscan EUR European +ERR188318 HG00276 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123424 FIN Finnish EUR European +ERR188319 NA12249 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125371 CEU CEPH EUR European +ERR188320 HG00185 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123648 FIN Finnish EUR European +ERR188321 HG00339 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123991 FIN Finnish EUR European +ERR188322 NA19190 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124041 YRI Yoruba AFR African +ERR188323 HG00257 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123047 GBR British EUR European +ERR188324 NA07347 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123572 CEU CEPH EUR European +ERR188325 NA06984 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124763 CEU CEPH EUR European +ERR188326 HG00275 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123421 FIN Finnish EUR European +ERR188327 NA06985 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124762 CEU CEPH EUR European +ERR188328 HG00109 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125160 GBR British EUR European +ERR188329 NA20505 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124359 TSI Tuscan EUR European +ERR188330 HG00379 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124746 FIN Finnish EUR European +ERR188331 NA12155 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124955 CEU CEPH EUR European +ERR188332 HG00158 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124585 GBR British EUR European +ERR188333 HG00238 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124131 GBR British EUR European +ERR188334 NA20543 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125149 TSI Tuscan EUR European +ERR188335 NA20798 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123821 TSI Tuscan EUR European +ERR188336 NA12004 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125144 CEU CEPH EUR European +ERR188337 HG00127 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122871 GBR British EUR European +ERR188338 HG00134 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE FALSE GEUVADIS SAME123067 GBR British EUR European +ERR188339 NA12815 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123022 CEU CEPH EUR European +ERR188340 HG00353 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125120 FIN Finnish EUR European +ERR188341 HG00328 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123799 FIN Finnish EUR European +ERR188342 HG00111 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125340 GBR British EUR European +ERR188343 NA20589 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122865 TSI Tuscan EUR European +ERR188344 NA18868 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124910 YRI Yoruba AFR African +ERR188345 NA20771 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124577 TSI Tuscan EUR European +ERR188346 HG00312 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE FALSE GEUVADIS SAME124336 FIN Finnish EUR European +ERR188347 NA20525 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124015 TSI Tuscan EUR European +ERR188348 NA11995 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123968 CEU CEPH EUR European +ERR188349 NA12842 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123542 CEU CEPH EUR European +ERR188350 NA12399 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124193 CEU CEPH EUR European +ERR188351 HG00253 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123051 GBR British EUR European +ERR188352 NA18909 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123561 YRI Yoruba AFR African +ERR188353 NA20586 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122864 TSI Tuscan EUR European +ERR188354 NA12775 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124257 CEU CEPH EUR European +ERR188355 HG00267 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123577 FIN Finnish EUR European +ERR188356 NA20514 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124558 TSI Tuscan EUR European +ERR188357 NA20517 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124557 TSI Tuscan EUR European +ERR188358 HG00367 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124540 FIN Finnish EUR European +ERR188359 NA20537 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE FALSE GEUVADIS SAME124168 TSI Tuscan EUR European +ERR188360 NA20787 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123609 TSI Tuscan EUR European +ERR188361 HG00189 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123640 FIN Finnish EUR European +ERR188362 HG00371 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124747 FIN Finnish EUR European +ERR188363 NA19206 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122983 YRI Yoruba AFR African +ERR188364 NA19248 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123681 YRI Yoruba AFR African +ERR188365 NA19117 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124914 YRI Yoruba AFR African +ERR188366 HG00264 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123578 GBR British EUR European +ERR188367 NA19102 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125112 YRI Yoruba AFR African +ERR188368 HG00105 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123949 GBR British EUR European +ERR188369 NA20512 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124560 TSI Tuscan EUR European +ERR188370 HG00240 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123221 GBR British EUR European +ERR188371 NA11920 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124901 CEU CEPH EUR European +ERR188372 NA20807 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125363 TSI Tuscan EUR European +ERR188373 NA18870 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125101 YRI Yoruba AFR African +ERR188374 HG00360 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124539 FIN Finnish EUR European +ERR188375 NA18858 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124730 YRI Yoruba AFR African +ERR188376 NA07037 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122862 CEU CEPH EUR European +ERR188377 NA12045 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123211 CEU CEPH EUR European +ERR188378 HG00259 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123056 GBR British EUR European +ERR188379 HG00148 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124388 GBR British EUR European +ERR188380 NA20502 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124358 TSI Tuscan EUR European +ERR188381 NA20769 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124371 TSI Tuscan EUR European +ERR188382 NA20536 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124167 TSI Tuscan EUR European +ERR188383 HG00136 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123065 GBR British EUR European +ERR188384 NA20795 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123818 TSI Tuscan EUR European +ERR188385 HG00138 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123059 GBR British EUR European +ERR188386 NA20521 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124018 TSI Tuscan EUR European +ERR188387 HG00160 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124780 GBR British EUR European +ERR188388 NA12341 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125158 CEU CEPH EUR European +ERR188389 NA10851 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125317 CEU CEPH EUR European +ERR188390 NA19235 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125002 YRI Yoruba AFR African +ERR188391 HG01789 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124433 GBR British EUR European +ERR188392 NA19210 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125383 YRI Yoruba AFR African +ERR188393 NA20772 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124574 TSI Tuscan EUR European +ERR188394 NA20813 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125189 TSI Tuscan EUR European +ERR188395 HG00365 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124542 FIN Finnish EUR European +ERR188396 NA12383 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124384 CEU CEPH EUR European +ERR188397 HG00271 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123417 FIN Finnish EUR European +ERR188398 NA20535 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124166 TSI Tuscan EUR European +ERR188399 NA20531 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124170 TSI Tuscan EUR European +ERR188400 HG00188 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123641 FIN Finnish EUR European +ERR188401 HG00141 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124395 GBR British EUR European +ERR188402 NA20581 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122859 TSI Tuscan EUR European +ERR188403 HG00131 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123064 GBR British EUR European +ERR188404 NA12750 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124646 CEU CEPH EUR European +ERR188405 NA20799 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123822 TSI Tuscan EUR European +ERR188406 NA20828 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123076 TSI Tuscan EUR European +ERR188407 HG01790 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124222 GBR British EUR European +ERR188408 NA20810 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125192 TSI Tuscan EUR European +ERR188409 NA18923 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123205 YRI Yoruba AFR African +ERR188410 NA12156 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124952 CEU CEPH EUR European +ERR188411 HG00243 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123224 GBR British EUR European +ERR188412 HG00129 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122867 GBR British EUR European +ERR188413 NA12890 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124116 CEU CEPH EUR European +ERR188414 NA12043 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123214 CEU CEPH EUR European +ERR188415 NA12058 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123416 CEU CEPH EUR European +ERR188416 HG00102 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123945 GBR British EUR European +ERR188417 HG00327 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123791 FIN Finnish EUR European +ERR188418 HG00326 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123792 FIN Finnish EUR European +ERR188419 NA20800 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125364 TSI Tuscan EUR European +ERR188420 NA12763 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123872 CEU CEPH EUR European +ERR188421 NA19225 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125218 YRI Yoruba AFR African +ERR188422 NA19172 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124420 YRI Yoruba AFR African +ERR188423 NA19107 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123393 YRI Yoruba AFR African +ERR188424 NA20819 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125183 TSI Tuscan EUR European +ERR188425 HG00187 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123646 FIN Finnish EUR European +ERR188426 NA11843 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125140 CEU CEPH EUR European +ERR188427 NA19159 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124716 YRI Yoruba AFR African +ERR188428 HG00099 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123271 GBR British EUR European +ERR188429 NA12889 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123951 CEU CEPH EUR European +ERR188430 HG00132 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123061 GBR British EUR European +ERR188431 NA12273 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123256 CEU CEPH EUR European +ERR188432 HG00309 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124160 FIN Finnish EUR European +ERR188433 NA11829 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124761 CEU CEPH EUR European +ERR188434 NA19209 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122994 YRI Yoruba AFR African +ERR188435 NA11830 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124553 CEU CEPH EUR European +ERR188436 NA20540 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125148 TSI Tuscan EUR European +ERR188437 NA20803 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125367 TSI Tuscan EUR European +ERR188438 NA12272 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123231 CEU CEPH EUR European +ERR188439 HG00329 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123798 FIN Finnish EUR European +ERR188440 NA19200 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122989 YRI Yoruba AFR African +ERR188441 NA12348 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125163 CEU CEPH EUR European +ERR188442 NA18910 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123402 YRI Yoruba AFR African +ERR188443 HG00130 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123063 GBR British EUR European +ERR188444 NA19129 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125021 YRI Yoruba AFR African +ERR188445 HG00173 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124960 FIN Finnish EUR European +ERR188446 NA12347 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125316 CEU CEPH EUR European +ERR188447 NA18934 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123036 YRI Yoruba AFR African +ERR188448 HG00244 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123217 GBR British EUR European +ERR188449 NA18499 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124059 YRI Yoruba AFR African +ERR188450 HG00235 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124122 GBR British EUR European +ERR188451 NA19149 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124605 YRI Yoruba AFR African +ERR188452 NA20515 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124559 TSI Tuscan EUR European +ERR188453 NA20529 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124011 TSI Tuscan EUR European +ERR188454 NA19207 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122984 YRI Yoruba AFR African +ERR188455 HG00146 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124390 GBR British EUR European +ERR188456 HG00249 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE FALSE GEUVADIS SAME123227 GBR British EUR European +ERR188457 HG00280 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122831 FIN Finnish EUR European +ERR188458 NA20516 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124556 TSI Tuscan EUR European +ERR188459 NA19143 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124609 YRI Yoruba AFR African +ERR188460 NA19153 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123019 YRI Yoruba AFR African +ERR188461 HG00126 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME122872 GBR British EUR European +ERR188462 HG00375 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124750 FIN Finnish EUR European +ERR188463 NA19247 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123691 YRI Yoruba AFR African +ERR188464 HG00252 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123052 GBR British EUR European +ERR188465 HG00112 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125341 GBR British EUR European +ERR188466 HG00142 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124818 GBR British EUR European +ERR188467 NA12286 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124642 CEU CEPH EUR European +ERR188468 HG00154 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124587 GBR British EUR European +ERR188469 HG01334 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123533 GBR British EUR European +ERR188470 HG02215 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123904 GBR British EUR European +ERR188471 NA19130 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125229 YRI Yoruba AFR African +ERR188472 HG00378 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124745 FIN Finnish EUR European +ERR188473 HG00344 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125255 FIN Finnish EUR European +ERR188474 NA07051 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124378 CEU CEPH EUR European +ERR188475 NA20815 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME125187 TSI Tuscan EUR European +ERR188476 NA19093 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME123172 YRI Yoruba AFR African +ERR188477 NA12778 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124249 CEU CEPH EUR European +ERR188478 HG01791 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124221 GBR British EUR European +ERR188479 NA20761 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124363 TSI Tuscan EUR European +ERR188480 HG00362 female LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124537 FIN Finnish EUR European +ERR188481 NA07048 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124188 CEU CEPH EUR European +ERR188482 HG00308 male LCL naive LCL 0 75bp FALSE TRUE poly(A) TRUE TRUE GEUVADIS SAME124161 FIN Finnish EUR European diff --git a/test_data/GEUVADIS_test_input.tsv b/test_data/GEUVADIS_test_input.tsv new file mode 100644 index 0000000..21668cc --- /dev/null +++ b/test_data/GEUVADIS_test_input.tsv @@ -0,0 +1,6 @@ +dataset_id 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a/test_data/exon/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz b/test_data/exon/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz new file mode 100755 index 0000000..a16d3a1 Binary files /dev/null and b/test_data/exon/exon_counts_Ensembl_105_phenotype_metadata.tsv.gz differ diff --git a/test_data/exon/exon_sumstats_files.txt b/test_data/exon/exon_sumstats_files.txt new file mode 100644 index 0000000..524de71 --- /dev/null +++ b/test_data/exon/exon_sumstats_files.txt @@ -0,0 +1 @@ +/gpfs/helios/home/kerimov/alasoo_lab/plotgen/test_data/exon/QTD000111_chr_22_18500000_20000000.parquet diff --git a/test_data/ge/QTD000110.credible_sets.chr22.subset.parquet b/test_data/ge/QTD000110.credible_sets.chr22.subset.parquet new file mode 100644 index 0000000..09322aa Binary files /dev/null and b/test_data/ge/QTD000110.credible_sets.chr22.subset.parquet differ diff --git a/test_data/ge/QTD000110_chr_22_16067822_21318750.parquet b/test_data/ge/QTD000110_chr_22_16067822_21318750.parquet new file 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file mode 100644 index 0000000..393db9c --- /dev/null +++ b/test_data/tx/exon_sumstats_files.txt @@ -0,0 +1 @@ +/gpfs/helios/home/kerimov/alasoo_lab/plotgen/test_data/tx/QTD000111_exon_for_tx_chr_22_18500000_20000000.parquet diff --git a/test_data/tx/transcript_usage_Ensembl_105_phenotype_metadata.tsv.gz b/test_data/tx/transcript_usage_Ensembl_105_phenotype_metadata.tsv.gz new file mode 100755 index 0000000..4065fcb Binary files /dev/null and b/test_data/tx/transcript_usage_Ensembl_105_phenotype_metadata.tsv.gz differ diff --git a/test_data/txrev/GEUVADIS_txrev_chr22_test_input.tsv b/test_data/txrev/GEUVADIS_txrev_chr22_test_input.tsv new file mode 100644 index 0000000..a145b49 --- /dev/null +++ b/test_data/txrev/GEUVADIS_txrev_chr22_test_input.tsv @@ -0,0 +1,2 @@ +dataset_id study_id quant_method qtl_group study_name credible_sets_file sample_meta vcf_file coverage_path usage_matrix_norm tpm_matrix exon_summ_stats_files all_summ_stats_files pheno_meta scaling_factors +QTD000113 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/dev/null +++ b/test_data/txrev/all_sumstats_files.tsv @@ -0,0 +1 @@ +/gpfs/helios/home/kerimov/alasoo_lab/plotgen/test_data/txrev/QTD000113_chr_22_18500000_20000000.parquet diff --git a/test_data/txrev/exon_sumstats_files.txt b/test_data/txrev/exon_sumstats_files.txt new file mode 100644 index 0000000..7c67703 --- /dev/null +++ b/test_data/txrev/exon_sumstats_files.txt @@ -0,0 +1 @@ +/gpfs/helios/home/kerimov/alasoo_lab/plotgen/test_data/txrev/QTD000111_exon_for_txrev_chr_22_18500000_20000000.parquet diff --git a/test_data/txrev/txrevise_Ensembl_105_phenotype_metadata.tsv.gz b/test_data/txrev/txrevise_Ensembl_105_phenotype_metadata.tsv.gz new file mode 100755 index 0000000..a05d28e Binary files /dev/null and b/test_data/txrev/txrevise_Ensembl_105_phenotype_metadata.tsv.gz differ