jamesemery

We already have a battery of carrot tests that we would like to run to evaluate the HaplotypeCaller. However those tests do not currently cover any of the new use...

Revisit "Jumbo"Annotations and find a more descriptive name

1

Recently for Mutect a new class of `JumboInfoFieldAnnotations` and `JumboGenotypeAnntations` were introduced into GATK and their names are somewhat misleading and confusing on first pass. I would suggest renaming them...

Added a slightly more helpful error message to the reads filter

3

Fixes #7944

I have noticed after looking at the HaplotypeCaller command line in some recent forum posts (https://gatk.broadinstitute.org/hc/en-us/community/posts/7293912288795-Haploytpe-caller-shows-me-that-0-read-s-were-filtered-by-MappingQualityAvailableReadFilter-etc) that the output of the filtering summary can be confusing if a lot of...

Investigate potential memory leak in GKL + HaplotypeCaller when running long intervals

1

I recently noticed a series of what were evidently memory failures when running HaplotypeCaller on some standard test WGS data when using the exact task used in the warp pipeline...

Reverting the CombineGVCFs and GenotypeGVCFs to the old behavior for no-calls when there are no PLs present.

2

Initial check-in to find test failures. Adresses #8328