The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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.