How to get population specific SNPs from a vcf file
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6 weeks ago
291796256 • 0

I've got a vcf file and There are 500 individuals in it.Of these 500 individuals, 30 individuals form group A.How can i get all SNPs specific to GroupA (Present in at least one of the 30 individuals and not in the remaining 470).

Looking forward to your answer.

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specific SNPs population • 234 views
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Entering edit mode
6 weeks ago
bcftools view --samples-file list-in-groupA.txt -O u in.vcf | bcftools view -i 'AC>0'
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