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Hi all, I am using `gatk VariantFiltration` to filter my GBS data. I need to set a threshold for the missing rate, such as 0.7. I know I can use...

dongyiyi

test java 21

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- update to gradle 8.4 and build with java 21 - fixing or supressing various warnings - in progress - allow warnings and update actions to 21 so we can...

lbergelson

Azure URIs and GenomicsDB

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@lbergelson, just want to discuss some issues here- 1. We currently have to use `--avoid-nio` with `--sample-name-map` and `--bypass-feature-reader` to get `GenomicsDBImport` to work with azure URIs. Why don't we...

nalinigans

Conda repository changes affecting local installs of earlier versions of GATK (Forum post included)

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Hi We have a forum post asking help for getting GATK 4.1.0.0 conda environment installed using the yml file. [https://gatk.broadinstitute.org/hc/en-us/community/posts/18332470602523-Install-GATK-version-4-1-0-0-using-Conda-](url) Looks like restructuring of the default repository under conda took...

gokalpcelik

DRAGEN Joint Detection DO NOT MERGE

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Initial implementation of DRAGEN joint detection. Functional equivalence with respect to DRAGEN joint detection is actually worse than before due to many outstanding questions. We currently have no idea how...

davidbenjamin

We need a way to read files from azure in our tests. This means one of: 1. adding a service account (or whatever the azure equivalent is) and the ability...

lbergelson

ValidateVariants memory usage is high when using a gvcf as the interval list

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`ValidateVariants` requires a large amount of memory (>16Gb) to validate a GVCF when another GVCF is used as the interval list. This is not the case if a regular interval...

meganshand

Add hardclip segments option to SplitNCigarReads tool

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Currently the GATK4 version of SplitNCigarReads softclips the overlapping segments of the reads across the split segments. This is a departure from the original GAKT3 behavior which hardclipped the edges....

jamesemery

Add annotation checks to ValidateVariants

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Ideally for GnarlyGenotyper inputs and outputs, check to make sure required Gnarly annotations are present, AS annotation lengths are correct, necessary VQSR annotations are present.

ldgauthier

Adding VCF index argument to SelectVariants

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## Feature request ### Tool(s) or class(es) involved `SelectVariants` ### Description In order to run SelectVariants with VCF inputs that are in separate locations from their index files or to...

meganshand