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Mirror of Picard metrics documentation generation changes.

2

Reflect the changes from https://github.com/broadinstitute/picard/pull/1782 in the GATK doc build. Note that this requires a new version of Picard that is not yet released. Also, I suppressed deprecation warnings caused...

cmnbroad

dummy PR for carrot testing **DO NOT MERGE**

44

jamesemery

I am doing somatic variant calling for whole genome sequencing. This tool could be improved to have reasonable RAM demands. ``` #PBS -l walltime=05:00:00,ncpus=26,mem=750GB #PBS -q hugemem ``` Fails after...

DarioS

Integration tests are not passing as the gold files have not been updated. Understanding what "correct" looks like for spanning deletions beyond just unit tests is very complex, and fraught...

kcibul

Address log4j vulnerability in workflows

4

[Tag 4.2.4.0](https://github.com/broadinstitute/gatk/releases/tag/) doesn't appear to address the fact that WDLs still reference older GATK Docker images and therefore are still vulnerable. This is a quick replacement of all references to...

aofarrel

Initial support for spanning deletions and refactoring for testability

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**Spanning Deletion Changes** 1. Created a new SpanningDeletionRecord as a subclass of ReferenceRecord but allows us to store GT and GQ 2. in handlePotentialSpanningDeletion when processing a deletion, we create...

kcibul

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...

jamesemery

## Feature request ### Tool(s) or class(es) involved Docker image ### Description We've been using this function in the GATK-SV WDLs to estimate the appropriate `-XmX` Java parameter for GATK...

mwalker174

Funcotator Exception: String index out of range

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This request was created from a contribution made by Mark Godek on May 28, 2020 12:43 UTC. Link: https://gatk.broadinstitute.org/hc/en-us/community/posts/360067471451-Funcotator-cannot-complete-funcotaion-for-variant-due-to-alternate-allele -- I'm attempting to annotate germline variants after VQSR with Funcotator...

GATKSupportTeam

## Bug Report Hi, we are using the dockstore version of the GATK variant calling pipeline that leverages mutect 2: [github.com/broadinstitute/gatk/mutect2:4.1.8.1](https://dockstore.org/workflows/github.com/broadinstitute/gatk/mutect2:4.1.8.1) We're processing human glioma data, and currently we are...

mschachter