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!