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Concordance tool for somatic variant calling

5

This ticket is for tracking the progress of the concordance project described here which is in collaboration with @davidbenjamin from DSP. The output of GATK Mutect2 is in VCF format,...

amithasandur

Closes #7353.

davidbenjamin

Upgrade samtools in the GATK docker image to 1.10 (at least)

1

## Feature request ### Tool(s) or class(es) involved The docker image would need to be updated (gatkbase docker image). See line ~17 in `scripts/docker/gatkbase/Dockerfile` ### Description Can you include a...

LeeTL1220

AS_FilterStatus uses an incorrect number of fields for some records

12

## Bug Report ### Affected tool Mutect2 ### Affected versions - [x] Latest public release version 4.1.8.1 - [x] Latest master branch as of 9/20/2020 ### Description Mutect2’s header defines...

DonFreed

VS-227 clean up temp tables

5

Previously, a temporary table is created as part of extract of the VQSR features, and it goes into a separate `temp_tables` dataset in the current project -- that is no...

RoriCremer

GenotypeGVCFs/GenomicsDB and Cannot allocate memory error

36

Hello, We're trying to run GenotypeGVCFs on a large genomicsDB workspace. The command is below, with the output. We run these jobs scatter/gather, with each job getting a define, small...

bbimber

expansion hunter pre processor

2

tedsharpe

Mutect2 extremely slow in force-calling mode

2

## Bug Report ### Affected tool(s) or class(es): Mutect2 ### Affected version(s) gatk 4.2.5 ### Description Like most use cases, I acquired a high-confidence, "consensus" VCF from a large batch...

haochenz96

java.lang.ArrayIndexOutOfBoundsException when creating tabix index

4

## Bug Report ### Affected tool(s) or class(es) gatk SortVcf ### Affected version(s) Mac OS X 10.16 x86_64; OpenJDK 64-Bit Server VM 1.8.0_322-b06; Deflater: Intel; Inflater: Intel; Provider GCS is...

bw2

Mutect2 error ComparableSamRecordIterator

1

## Bug Report ### Affected tool(s) or class(es) Mutect2 in tumour-normal mode ### Affected version(s) - 4.2.6.1 - 4.2.0.0 ### Description Mutect2 crashes with an error: ``` 16:53:19.984 INFO Mutect2...

ashakru