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Is VariantAnnotator compatible with the GVCF workflow?
In the Best Practices for Germline SNP & Indel Discovery in Whole Genome and Exome Sequence, https://software.broadinstitute.org/gatk/best-practices/bp_3step.php?case=GermShortWGS&p=2,
the steps are listed as:
Map to reference with BWA mem - Mark duplicates with Picard - Base quality score recalibration
Generate GVCF per-sample with HaplotypeCaller - Perform joint genotyping - Filter variants
(Optional) Refine genotypes - Annotate variants - Evaluate callset
However, after step 2, we have a multi-sample VCF file. But, in step 3, it is suggested to use VariantAnnotator to annotate the variants, but in the tool documentation it seems VariantAnnotator accepts VCF files (not GVCF files) and seems to assume they are single-sample VCF files.