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GATK v3.0 not forwarding GVCF genotype annotations?

bredesonbredeson Member Posts: 33
edited March 2014 in Ask the GATK team

GATK Team,

First of all, I'm very excited about v3.x GATK, you guys and gals on the GATK Team are doing awesome work!

I have a question: How do I get CombineGVCFs to forward the sample-level annotations calculated by HC with the --emitRefConfidence GVCF option enabled? I tried passing the same annotation flags to CombineGVCFs that I passed to HC, but none of the annotations beyond the standard set were incorporated. Annotations such as StrandBiasBySample require access to the underlying reads and forwarding these annotations to the CombineGVCFs output would be less prohibitive than running VariantAnnotator on my 20 WGS datasets...

Post edited by Geraldine_VdAuwera on

Best Answer


  • bredesonbredeson Member Posts: 33

    Thanks @Geraldine_VdAuwera‌, this would be very helpful :-)

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,713 admin

    Ah, so I'm told that the sample-level annotations are getting forwarded normally by CombineGVCFs. If you're seeing a different behavior, can you please post your command line and a couple of before/after records?

    Geraldine Van der Auwera, PhD

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