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Question: GATK GermlineCNVCaller & PostprocessGermlineCNVCalls
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Hi, I was wondering if anyone here has experience in running GATK GermlineCNVCaller & PostprocessGermlineCNVCalls for calling CNVs in germline samples?

The VCF files that I'm getting always have ALT to be "< DEL>,< DUP>". Shouldn't ALT be just one of them or neither? Somehow both the interval and segment VCF files I'm looking at have all positions marked as "< DEL>,< DUP>".

If anyone here has experience with this, I would really appreciate some feedback. Thanks!

ADD COMMENTlink 10 months ago rajitz • 0

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