14_pgs_cell_line_submission.sh

#!/bin/bash 
#SBATCH -J cell-line-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"
pgs_results_dir="/well/lindgren/UKBIOBANK/dpalmer/PRS_cell_data/data/PGS_score_results"
pgs_score_dir="/well/lindgren/UKBIOBANK/dpalmer/PRS_cell_data/data/PGS_score_files"
imputed_path="/well/lindgren/UKBIOBANK/dpalmer/PRS_cell_data/data/celldataB37/HRC/imputed"
mkdir -p ${pgs_results_dir}/cell_line_job_${SLURM_ARRAY_TASK_ID}

pgs-calc apply \
	--ref ${pgs_score_dir}/pgs-catalog-20221123-hg19/scores/job_${SLURM_ARRAY_TASK_ID}.txt \
	${imputed_path}/chr*_UKB_cell_line_1000G_intersected.dose.vcf.gz \
	--out ${pgs_results_dir}/cell_line_job_${SLURM_ARRAY_TASK_ID}/cell_line_intersect_UKB_1000G_job_${SLURM_ARRAY_TASK_ID}_scores.txt \
	--dbsnp /well/lindgren/UKBIOBANK/dpalmer/PRS_cell_data/data/dbsnp154_hg19.txt.gz \
	--report-html ${pgs_results_dir}/cell_line_job_${SLURM_ARRAY_TASK_ID}/cell_line_intersect_UKB_1000G_job_${SLURM_ARRAY_TASK_ID}_scores_report.html \
	--genotypes GT \
	--meta ${pgs_score_dir}/pgs-catalog-20221123-hg19/scores.meta.json \
	--report-csv ${pgs_results_dir}/cell_line_job_${SLURM_ARRAY_TASK_ID}/cell_line_intersect_UKB_1000G_job_${SLURM_ARRAY_TASK_ID}_scores_report.csv