about GATK VariantAnnotator and VCF files

Question

[Bogdan]

Dear all,

talking about VariantAnnotator in GATK : https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_annotator_VariantAnnotator.php, please could you advise :

could it be safely used on VCF files produced by other callers like STRELKA, VIRMID, Varscan2 etc ...beside MUTECT1 or MUTECT2 ? I am referring to the use of VariantAnnotator with the options for FS, SOR, RMSMappingQuality, QualByDepth, ReadPosRankSumTest ...

or, are there any minimal requirements for a VCF file produced by other somatic mutation callers in order to be fully annotated by VariantAnnotator ?

thank you,

-- bogdan

Answer 1

[Sean Davis]

GATK VariantAnnotator can be used for VCFs from somatic variant callers as well.