filter out subset of samples from vcf file

Question

[mab658]

I have a very big compressed vcf file with over 8000 samples. I wanted to extract out data for those samples whose name start with first three characters "TMS" so that I can have a new vcf file with those samples and their variants data only. Could anyone help me out with the vcftools or bcftools command to accomplish this? Thanks

Answer 1

[Pierre Lindenbaum]

gunzip -c in.vcf.gz | grep "#CHROM" -m 1  | cut -f 10- | tr "\t" "\n" | grep ^TMS > samples.txt

bcftools view --samples-file  samples.txt  in.vcf.gz

[finswimmer]

zgrep "#CHROM"... ;)

[mab658]

Thanks Pierre. I am able to extract out the samples. All works fine.

[Pierre Lindenbaum]

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