tensorQTL workflow

Portable QTL mapper

tensorQTL workflow uses GPU-enabled tensorqtl QTL mapper: Taylor-Weiner, Aguet, et al., Genome Biol. 20:228, 2019

Usage examples

For testing

nextflow run tensorQTL.nf -profile tartu_hpc,testing_tartu_hpc -resume

Pipeline should create the following files in your working directory:

work            # Directory containing the nextflow working files
testing_results/GEUVADIS_test_samples         # Finished testing results (containing one 204M sized .parquet file)

Running the analysis

nextflow run tensorQTL.nf -profile tartu_hpc -resume\
 --dataset GEUVADIS\
 --vcf_prefix_path ~/tensorQTL_workflow/tensorQTL/data/testing_data/GEUVADIS_chr1_212626194_212851227_testing_samples\
 --covariates ~/tensorQTL_workflow/tensorQTL/data/testing_data/GEUVADIS_LCL_cells.covariates_added_sex_test_samples.txt\
 --expression_file ~/tensorQTL_workflow/tensorQTL/data/testing_data/GEUVADIS.LCL_naive_test_samples.tsv\
 --sample_genotype_ids ~/tensorQTL_workflow/tensorQTL/data/testing_data/GEUVADIS_LCL_study_ids_test_samples.txt\
 --only_autosomal_chr false\
 --outputpath ~/results\
 --median_tpm_filtration_file ~/tensorQTL_workflow/tensorQTL/data/LCL_naive_median_tpm_filtered_genes.tsv.gz

Optional arguments/info

• --vcf_prefix_path : path to vcf file and its indexed file, example: ~/BLUEPRINT/BLUEPRINT.MAF001, /BLUEPRINT folder has to contain files: BLUEPRINT.MAF001.vcf.gz and BLUEPRINT.MAF001.vcf.gz.csi
• --covariates : covariates file, from qtlmap workflow
• --vcf_genotype_field : DS or GT, default= DS
• --maf_filter : MAF filter, default = 0.01
• --sample_genotype_ids : file with sample id and matching genotype id, with header
• --pvalue : to filter out results by p-value, default: 1
• --only_autosomal_chr : boolean, if false includes regions from X chr, default: true
• --batf3_region_only : boolean, to run only testing region 1:212626194-213256972.
• --median_tpm_filtration_file : median tpm file to filter genes, needed to speed up analysis, otherwise includes all genes. Files are: data/LCL_naive_median_tpm_filtered_genes.tsv.gz or data/T-cell_median_tpm_filtered_genes.tsv.gz (for naive LCL or T-cells)