example

#### Yogasudha Veturi 07Jan2021

# DOWNLOAD DATA HERE: https://ritchielab.org/files/Lipid_Pleiotropy_project/gene_level_coloc_example_data.tar.gz


path=$PWD
path_gwas=$PWD/harmonized_gwas
path_gtex=$PWD/GTEx
reference_folder=$PWD/reference_data
output_folder=$PWD/output
mkdir $PWD/out

input=Input_gene_trait_tissue_data_ensg.txt
genes_list=($(awk '{print $1}' ${input}))
traits_list=($(awk '{print $2}' ${input}))
tissues_list=($(awk '{print $3}' ${input}))
datasets_list=($(awk '{print $4}' ${input}))
ensg_list=($(awk '{print $5}' ${input}))
chr_list=($(awk '{print $6}' ${input}))
genes_file=ENSG_start_stop_chr_gene_mart_export.txt
eqtl_sample_size_file=GTEx_v8_PredictDB_tissues_num_samples.txt
lines=`expr $(< "$input" wc -l) - 1`

for i in $( seq 0 $lines )
do
dataset=${datasets_list[${i}]}
tissue=${tissues_list[${i}]}
trait=${traits_list[${i}]}
gene=${genes_list[${i}]}
ensg=${ensg_list[${i}]}
chr=${chr_list[${i}]}

Rscript ../run_gene_level_coloc.R \
--gwas_data_name=${dataset} \
--trait=${trait} \
--tissue=${tissue} \
--gene_of_interest=${ensg} \
--run_cojo=FALSE \
--cojo_maf=0.01 \
--chr=${chr} \
--coloc_p1=1e-04 \
--coloc_p2=1e-04 \
--coloc_p12=1e-06 \
--lead_snp_window_size=200000 \
--gene_boundary_window_size=1000000 \
--gwas_p_threshold=0.0001 \
--eqtl_p_threshold=0.0001 \
--gwas_response_type="quant" \
--gwas_file=${path_gwas}/${dataset}_${trait}_GWAS_harmonized.txt.gz \
--genes_file=${genes_file} \
--output_folder=${output_folder} \
--reference_folder=${reference_folder} \
--eqtl_folder=${path_gtex} \
--eqtl_sample_size_file=${path_gtex}/${eqtl_sample_size_file} &> out/geneLevelColoc_${i}.log
echo "$i"
done