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Fix bug in FilterMutectCalls 'haplotype' filter by checking PGT and make --linked-de-bruijn-graph default

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This request was created from a contribution made by Francesco Mazzarotto on March 23, 2022 14:16 UTC. Link: [https://gatk.broadinstitute.org/hc/en-us/community/posts/4892502642075-FilterMutectCalls-haplotype-filter-value-assigned-to-variants-with-different-PGT-tag](https://gatk.broadinstitute.org/hc/en-us/community/posts/4892502642075-FilterMutectCalls-haplotype-filter-value-assigned-to-variants-with-different-PGT-tag) \-- Hello, I am using GATK v4.2.5.0 to process tumor-only samples...

GATKSupportTeam

Mutect2 WDL: Funcotate task has useless variables - no way to increase memory for Funcotate task only

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## Bug/Usability Report ### Affected tool(s) or class(es) Mutect2 WDL ### Affected version(s) - [x] Latest public release version [4.1.81] - [x] Latest master branch as of October 28, 2021...

jason-cerrato

No quality in non-variant sites

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Heys, I am doing the SNP calling with Haplotypecaller BP_Resolution, CombineGVCFs with convert-to-base-pair-resolution and GenotypeGVCFs with include-non-variant-sites with GATK v.4.1.7.0 and when I get my vcf file, the non-variant sites...

gubrins

SV Pipeline Jobs LongRunning : BAFFromGVCFs_ImportGVCFs and GenotypeVCFs

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[GenomicsDB] As part of our pipeline, we are running the below mentioned command. What this step does is, reads the vcf files in batch of 50 so in total 4...

spatel-gfb

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

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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...

jamesemery

I believe `sites` and `variants` should be equivalent. I see that there is a warning emitted by GATK4 at sites that are not het, but it shouldn't be an error. If you're getting an error can you please post the full message in this thread?

5

I believe `sites` and `variants` should be equivalent. I see that there is a warning emitted by GATK4 at sites that are not het, but it shouldn't be an error....

Erich-Hartm

GenomicsDB excessive logging "[E::faidx_adjust_position] The sequence "chrX" was not found"

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## Bug Report ### Affected tool(s) or class(es) GenomicsDBImport ### Affected version(s) - [ ] Latest public release version [version?] - [x] Latest master branch as of Apr 4, 2022...

ldgauthier

Fix asynchronous Python exception propagation in StreamingPythonExecutor/CNNScoreVariants.

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Fix for https://github.com/broadinstitute/gatk/issues/7401. Draft mode for now until I do more verification.

cmnbroad

Test for presence of ack result message and simplify ProcessControllerAckResult API

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Fixes NPE reported in https://github.com/broadinstitute/gatk/issues/7811.

cmnbroad

multi-sample calling support in M2 WDL

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## Feature request ### Tool(s) or class(es) involved mutect2.wdl and related scripts ### Description It would be useful to have multi-sample calling support (#5560) in M2 WDL.

byoo