Filter multisample VCF for variants with less than N samples
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3.1 years ago
bjwiley23 ▴ 20

Hi,

Is there a tools which takes a multisample VCF, say for example 100 samples, and can take a param N=5 and only keep variants where <N samples have that variant?

I have searched bcftools and vcftools but cannot find there. I can do this with GATK VariantsToTable and then with logical in R but this seems like this is too simple of a task and that it too costly of time doing this way if I am going to do this over and over.

Brian

VCF • 530 views
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