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