Comparing calls from different VCFs
0
0
Entering edit mode
2.1 years ago
vctrm67 ▴ 20

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.

vcf maf • 769 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode

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”.

ADD REPLY
0
Entering edit mode

I have good experiences with hap.py.

ADD REPLY

Login before adding your answer.

Traffic: 2410 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6