Is there a way to take a difference of two VCF files? GATK can be used to take a Union or an Intersection, but I need the difference. There are two applications:
1. remove singletons. I have a VCF of all the SNPs and a VCF of the private ones. I need a VCF with the non-private SNPs.
2. get the non-CDS sequence. I can make a VCF of the exome SNPs by filtering against a gff file. I would also like to get the SNPs from non-CDS regions - which could be the difference of all SNPs and exome SNPs.
Any ideas, please?
University of Cambridge