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VQRS Crashing from no StrandOddsRatio Annotation

I have done a multisample call with UnifiedGenotyper and annotated with -A StrandOddsRatio (including several other annotations). When running VQRS filtering with the -an SOR tag it crashes because of incorrect annotation. The vcf file does not contain SOR annotation so this is correct. When using VariantAnnotator to correct this there's no tag to annotate with StrandOddsRatio.

Can I annotate a UnifiedGenotyper calls with StrandOddsRatio or am I missing something?


Best Answer


  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭


    I just tried running Variant Annotator on a vcf from Haplotype Caller, and the StrandOddsRatio annotation does get added. It will work for a vcf from Unified Genotyper too. You simply have to add -A StrandOddsRatio to your command. Also, you have to input the bam file along with the vcf.


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