Adds QD and AS_QD emission from VariantAnnotator on GVS input

broadinstitute / gatk

Official code repository for GATK versions 4 and up

https://software.broadinstitute.org/gatk

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Adds QD and AS_QD emission from VariantAnnotator on GVS input #8978

Closed meganshand closed 2 months ago

meganshand commented 2 months ago

Previously, AS_QD was ignored by VariantAnnotator since the annotate() function always returned an empty map. Now AS_QD will be added.

Also QD could only use QUAL as part of the calculation, but GVS output only contains the QUALapprox annotation. This change allows QD to be calculated from QUALapprox if QUAL is not present.