HaplotypeScore as an annotation for VariantRecalibrator after UnifiedGenotyper
The documentation on the HaplotypeScore annotation reads:
HaplotypeCaller does not output this annotation because it already evaluates haplotype segregation internally. This annotation is only informative (and available) for variants called by Unified Genotyper.
The annotation used to be part of the best practices:
I will include it in the VQSR model for UG calls from low coverage data. Is this an unwise decision? I guess this is for myself to evaluate. I thought I would ask, in case I have missed something obvious.