Entering edit mode
5.1 years ago
vctrm67
▴
80
Hi all,
Does anyone know of a way to compare mutation calls for two vcf files? The vcfs should be derived from the same dataset but I may have used a different caller than the other vcf, so I want to compare if the calls were good or what do they filter in general.
Compare how? If you just want to know if they contain the same calls, you can just use bedtools intersect.
That doesn't tell me what calls weren't included in the intersection that were in either vcf alone though, does it?
From the BEDtools 'intersect' documentation:
I have good experiences with hap.py.