Resolution of ambiguous calls in germline vcf
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7 weeks ago
Raygozak ★ 1.4k

Hi, I have a set of germline files from vcf generated by the gatk variant caller. What i'm seein when I annotate them using vcf2maf is that some mutations in two individuals have the same rsid but have start or end position off by one base in different individuals. There are several approaches that could be done.

I could just look up the rsid position and replace the "correct" one in all the samples.

I could just discard them and continue with the rest as usual.

try to resolve them but of course there could be thousands of them. Would looking at some field such as depth or do some filtering based on the number of samples be enough to decide what to do?

I'd appreciate your inputs on how to proceed.

Thanks

vcfs germline qc • 238 views
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