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09_pgs_ukb_submission.sh
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09_pgs_ukb_submission.sh
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#!/bin/bash
#SBATCH -J ukb-prs
#SBATCH -A lindgren.prj
#SBATCH -o output.out
#SBATCH -e error.err
#SBATCH -c 4
#SBATCH -p short
#SBATCH --array 1-33:1
#SBATCH --requeue
export PATH="/well/lindgren/dpalmer/:$PATH"
job=$SLURM_ARRAY_TASK_ID
mkdir /well/lindgren/UKBIOBANK/dpalmer/PRS_cell_data/data/PGS_score_results/ukb_job_${job}
pgs-calc apply --ref /well/lindgren/UKBIOBANK/dpalmer/PRS_cell_data/data/PGS_score_files/pgs-catalog-20221123-hg19/scores/job_${job}.txt /well/lindgren/UKBIOBANK/dpalmer/PRS_cell_data/data/UKB_imputed_subset/UKB_imputed_subset_chr*_thresholded_recode_merge_typed_final.vcf.gz --out /well/lindgren/UKBIOBANK/dpalmer/PRS_cell_data/data/PGS_score_results/ukb_job_${job}/ukb_job_${job}_scores.txt --dbsnp /well/lindgren/UKBIOBANK/dpalmer/PRS_cell_data/data/dbsnp154_hg19.txt.gz --report-html /well/lindgren/UKBIOBANK/dpalmer/PRS_cell_data/data/PGS_score_results/ukb_job_${job}/ukb_job_${job}_scores_report.html --genotypes GT --meta /well/lindgren/UKBIOBANK/dpalmer/PRS_cell_data/data/PGS_score_files/pgs-catalog-20221123-hg19/scores.meta.json --report-csv /well/lindgren/UKBIOBANK/dpalmer/PRS_cell_data/data/PGS_score_results/ukb_job_${job}/ukb_job_${job}_scores_report.csv