gatk

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This is a possible workaround for #7938. This isnt a finished PR, but I'm opening this to kick off tests.

bbimber

Adding scripts related to setting up haplotypecaller carrot regression tests.

2

jamesemery

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...

jamesemery

This method and a couple others in this class don't appear to have good test coverage,

dror27

Currently: // TODO NOTE this test is disabled. That is because currently it is difficult to generate ArtificialFlowBasedReads from scratch... @Test (enabled = false)

dror27

Codecov indicates that this new method is not covered by tests -- needs a test in IOUtilsUnitTes

dror27

Coverage analysis indicates that the new --assembly-complexity-reference-mode argument is not covered by tests.

dror27

Add XGBoostGqVariantFilter, a tool to recalibrate GQ

4

* Added MinGqVariantFilterBase * * loads VCF, pedigree, UCSC genome tract, and truth data * * calculates variant overlap with genome tracts * * forms matrices, tensors, and other helping...

TedBrookings

Default Mutect2 INFO field discrepancies between version 4.1.5.0 and 4.1.8.0

5

# Bug Report ### Affected tool(s) or class(es) _Mutect2_ ### Affected version(s) - [ ] 4.1.5.0 - [x] 4.1.8.0 ### Description INFO | 4.1.5 | 4.1.8 -----|-------|------- AS_SB_TABLE | ❌...

slw287r

Added a slightly more helpful error message to the reads filter

3

Fixes #7944

jamesemery