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I have a bunch of .vcf files in a folder and I want to run command below on all of them but doing that one by one manually is really painful. I am seeking for a way in terminal to do that simultaneously. The output would be a .txt file.
grep -v "##" /file.vcf | awk '{print $1"\t"$2"\t"$2"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11}' > /file.txt
Can you help please?
Assuming all your vcfs are in the same folder:
for file in *.vcf; do
grep -v "##" ${file} | awk '{print $1"\t"$2"\t"$2"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11}' > ${file}.txt
done
If additional CPUs are available:
CPU_COUNT=5
for file in *.vcf; do
(grep -v "##" ${file} | awk '{print $1"\t"$2"\t"$2"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11}' > ${file%.vcf}.txt) & let count+=1
[[ $((count%CPU_COUNT)) -eq 0 ]] && wait
done
one-liner:
CPU_COUNT=5; for file in *.vcf; do (grep -v "##" ${file} | awk '{print $1"\t"$2"\t"$2"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11}' > ${file%.vcf}.txt) & let count+=1; [[ $((count%CPU_COUNT)) -eq 0 ]] && wait; done
