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Old 04-26-2019, 10:29 AM   #1
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Location: Toronto

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Default GATK GermlineCNVCaller & PostprocessGermlineCNVCalls

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!
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