Here's the output on a test script:

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --cpus-per-task=40
#SBATCH --time=24:00:00
#SBATCH --job-name=1000Gchr1.8
#SBATCH --output=1000Gchr1.8.txt
#SBATCH --mail-type=ALL
#
#
#This script extracts 1000G samples using bcftools view for Sprime analysis
/scratch/t/tbviola/ckendall/Niagara_to_Keep/bcftools-1.10.2/./bcftools view --threads 40 --force-samples -S "/scratch/t/tbviola/ckendall/Niagara_to_Keep/Archaic_VCFs/ModernSamples/VCF/gNomad/gnomad.genomes.v3.1.2.hgdp_tgp.12.vcf.gz" -Oz -o "/scratch/t/tbviola/ckendall/Niagara_to_Keep/Archaic_VCFs/ModernSamples…

I was just wondering what I would need to do to get the sample names next to --force-samples -S instead of the chromosome. So the script output should look this:

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --cpus-per-task=40
#SBATCH --time=24:00:00
#SBATCH --job-name=1000Gchr1.8
#SBATCH --output=1000Gchr1.8.txt
#SBATCH --mail-type=ALL
#
#
#This script extracts 1000G samples using bcftools view for Sprime analysis
/scratch/t/tbviola/ckendall/Niagara_to_Keep/bcftools-1.10.2/./bcftools view --threads 40 "/scratch/t/tbviola/ckendall/Niagara_to_Keep/Archaic_VCFs/ModernSamples/VCF/gNomad/gnomad.genom…

I am thinking it probably needs these edits, but I want to make sure:

BCFToolsPath="$SCRATCH/Niagara_to_Keep/bcftools-1.10.2"
VCFPath="$SCRATCH/Niagara_to_Keep/Archaic_VCFs/ModernSamples/VCF/gNomad"
SamplesPath="$SCRATCH/Niagara_to_Keep/Archaic_VCFs/ModernSamples/VCF/1000GFiles/SprimeReady/Group1"
outputPath="$SCRATCH/Niagara_to_Keep/Archaic_VCFs/ModernSamples/VCF"


while read i; do
for ((chr=1; chr<=22; chr++)); do
command="$BCFToolsPath/./bcftools view"
chrVcf="$VCFPath/gnomad.genomes.v3.1.2.hgdp_tgp.$chr.vcf.gz"

I fixed it. Thank you sooooo much for your amazing help! You seriously saved me like a week's worth of work!

Here is the final:


while read i; do
for ((chr=1; chr<=22; chr++)); do
command="$BCFToolsPath/./bcftools view"
chrVcf="$VCFPath/gnomad.genomes.v3.1.2.hgdp_tgp.$chr.vcf.gz"
thisSamplePath="$SamplesPath/${i}_SprimeSamples.txt"
thisOutputPath="$outputPath/${i}.${chr}.vcf.gz"

printf '%s\n%s --threads 40 %s --force-samples -S %s -Oz -o %s\n' "$scriptHeader" \
"$command" \
"$chrVcf" \
"$thisSamplePath" \