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Clarify Gnarly required annotations

2

ldgauthier

LeftAlignAndTrimVariants doesn't work on MNPs

2

The documentation for `LeftAlignAndTrimVariants` indicates that it only works for indels. It should be updated to work for MNPs as well. This operation would simply remove any common leading bases...

jonn-smith

Merge master into ah var store

8

mcovarr

mutect2 4.2.6.1 fails in gvcf mode

6

Hello GATK team! ## Bug Report ### Affected tool(s) or class(es) mutect2 ### Affected version(s) - Latest public release version: 4.2.6.1 ### Description getting fail for all scatter task with...

jkobject

GenotypeGVCFs stuck at Starting traversal for coulple of days!!!

4

### Instructions The github issue tracker is for bug reports, feature requests, and API documentation requests. General questions about how to use the GATK, how to interpret the output, etc....

Bowen1992

Enable CSI index reading for bgzipped VCF files

7

## Feature request ### Tool(s) or class(es) involved Any tools that read VCF, but specifically GenotypeGVCFs ### Description I'm doing work where I'm working with genomes that have chromosomes that...

tfenne

Draft of GVS Cost observability WDL [VS-441]

1

mcovarr

Note to check on the inclusion of all binary files

RoriCremer

M2 does not emit GT

1

davidbenjamin

mutect2 homozygous alt GT annotation

4

## Feature request Running mutect2 (GATK v4.2.2) in tumor only mode on WES samples and asking it to use/keep germline and PON mutations. I have noticed that mutect never sets...

jkobject