Comparing calls from different VCFs

Question

[vctrm67]

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.

[jared.andrews07]

Compare how? If you just want to know if they contain the same calls, you can just use bedtools intersect.

[vctrm67]

That doesn't tell me what calls weren't included in the intersection that were in either vcf alone though, does it?

[harold.smith.tarheel]

From the BEDtools 'intersect' documentation:

There will likely be cases where you’d like to know which “A” features do not overlap with any of the “B” features. Perhaps you’d like to know which SNPs don’t overlap with any gene annotations. The -v (an homage to “grep -v”) option will only report those “A” features that have no overlaps in “B”.

[finswimmer]

I have good experiences with hap.py.