INTERVAL.sb

#!/bin/bash --login
# 14-12-2018 JHZ

#SBATCH -J bcftools
#SBATCH -o bcftools.log
#SBATCH -a 1-22
#SBATCH -t 3-0:0
#SBATCH -p long

export chr=$SLURM_ARRAY_TASK_ID

bcftools annotate --set-id "chr%CHROM\:%POS\_%REF\_%ALT" chr${chr}.vcf.gz -O z -o INTERVAL-${chr}.vcf.gz
plink --vcf INTERVAL-${chr}.vcf.gz --list-duplicate-vars require-same-ref -out INTERVAL-${chr}
awk '(NR>1){split($NF,dupids," ");print dupids[1]}' INTERVAL-${chr}.dupvar > INTERVAL-${chr}.dupid
plink --bfile INTERVAL-${chr} --exclude INTERVAL-${chr}.dupid --make-bed --out nodup-${chr}
awk -vOFS="\t" '
{
    CHR=$1
    POS=$4
    a1=$5
    a2=$6
    if (a1>a2) snpid="chr" CHR ":" POS "_" a2 "_" a1;
    else snpid="chr" CHR ":" POS "_" a1 "_" a2
    print snpid, $2
}' nodup-${chr}.bim > nodup-${chr}.snpid
plink --bfile nodup-${chr} --update-name nodup-${chr}.snpid 1 2 --make-bed --out UK10K1KG-${chr}