Set Difference in VCF Files

Question

[andrew.j.skelton73]

Hi,

Are there any ways to quickly find the set difference between two VCF Files? VCFTools compare allows me to find the intersection between two VCF files, but there doesn't seem to be an option for the set difference?

Any suggestions?

Thanks,

Answer 1

[Pierre Lindenbaum]

GATK selectVarant has an option --discordance: "Output variants not called in this comparison track"

I wrote a tool, VCFIn with an "exclude" option