Hi, I loaded two VCF files in two different objects with the readVCF function of VariantAnnotation. Is it possible to do an intersection e.g same chr, position ecc. between these two objects?

Thank you.

Riccardo

You might want to be more specific about the "etc" part. Otherwise, all I can say is "yes". But for example, to intersect by chr, position and alt, you could convert the VCF objects to VRanges and match:

vrA <- as(vcfA, "VRanges")
vrB <- as(vcfB, "VRanges")
vrA[vrA %in% vrB]

I guess we could make those operations work on VCF also.