Does callset derived from HyplotyperCaller need run through VariantAnnotator for VQSR step?

mikemike Posts: 103Member

Hi,

I just run HyplotypeCaller on a dataset. For the same dataset, I have run through Unified genotyper and then directly subjected the raw vcf from UG to VQSR step without the help of VariantAnnotator before and get through VQSR without any problem. However, when I try to subject the raw callset derived from HyplotypeCaller directly to VQSR step, the VQSR module complained about it and error message is below:

...

ERROR MESSAGE: Bad input: Values for HaplotypeScore annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See

http://gatkforums.broadinstitute.org/discussion/49/using-variant-annotator

So after HyplotypeCaller, the derived vcf file needs to run though VariantAnnotator? Since Unified genotyper derived callset does not need the help of VariantAnnotator (all annotations needed for VQSR are included after UG), it seems not the case for HyplotypeCaller? I can run through VariantAnnotator for HyplotypeCaller derived vcf file, just want to make sure if my understanding is correct?

Thanks and best

Mike

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,456Administrator, GATK Developer admin
    Answer ✓

    Hi Mike,

    It depends what annotations you are trying to recalibrate with. It is possible that some of the annotations you want were not added by the HaplotypeCaller. In that case you will indeed need to add them with VariantAnnotator.

    Please note that we no longer include HaplotypeScore in our recommendations for VQSR. This doe not mean you cannot use it, just that in our hands we have found it is not helpful.

    Geraldine Van der Auwera, PhD

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