dist-indels.sb

#!/bin/bash

#SBATCH --ntasks=1
#SBATCH --job-name=_indels
#SBATCH --time=12:00:00
#SBATCH --partition=medium
#SBATCH --array=1-228%5
#SBATCH --mem=128800
#SBATCH --output=dist/indels/_indels_%A_%a.out
#SBATCH --error=dist/indels/_indels_%A_%a.err
#SBATCH --export ALL

. /etc/profile.d/modules.sh
module load default-cardio
module load slurm
module load use.own

export TMPDIR=/scratch/jhz22/tmp
export p=$(awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"]+1{print $1}' sentinels/INF1_nold.sentinels)
export c=$(awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"]+1{print $2}' sentinels/INF1_nold.sentinels)
export r=$(awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"]+1{print $3}' sentinels/INF1_nold.sentinels)
export m=$(awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"]+1{print $4}' sentinels/INF1_nold.sentinels)
cat /scratch/jhz22/data/INTERVAL/INTERVAL.bim | \
awk -vchr=${c} -vpos=${r} '($1==chr && $4>=pos-1e6 && $4<pos+1e6){if (length($5)>1||length($6)>1) print $2}' > dist/indels/${p}-${m}.indels