Variant Quality Score Recalibration
Answered
Hi,
In gatk4, my understanding is that SnpEff has been superceded (now years ago). My question relates to cohort calling of hundreds of WES samples using the workflow. GenotypeGVCF has been run on the GenomicsDB to yield a joint vcf.
Are all required annotations for VariantRecalibrator now present following GenotypeGVCF? I know the Broad does not support SnpEff any longer but is there any value in adding external annotations prior to the VariantRecalibrator step using VariantAnnotator or Funcotator, or is it best to leave additional VCF annotation till later? I note Funcotator is specifically mentioned only for per-sample calling in the Best Practice Guidelines. Any experience with this would be appreciated.
Best,
Jakub
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Thank you for your post, Jakub S! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions.
Please see our Support Policy for more details about how we prioritize responding to questions.
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PS, for completeness: am aware of the following workflow https://gatk.broadinstitute.org/hc/en-us/articles/360035531112--How-to-Filter-variants-either-with-VQSR-or-by-hard-filtering.
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Hi Jakub S,
Regarding SnpEff and functional annotations, VQSR doesn't use any functional annotations to make the model. You can use any annotations that you prefer. If you want all of the standard annotations from GenotypeGVCFs, you can use the option -G StandardAnnotation and -G AS_StandardAnnotation.
Funcotator works on any VCF input, so it will work just fine on your joint VCF.
Please let us know if you have any other questions.
Best,
Genevieve
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