gatk

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GATK fails to genotype insertion immediately following a deletion at hg19:chr1:68896832

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## Bug Report ### Affected tool(s) or class(es) HaplotypeCaller ### Affected version(s) - [x] Latest public release version [4.1.6.0] - [ ] Latest master branch (not tested) ### Description I...

tfenne

Mutect2 is incompatible with Mutect2 VCFs as feature files

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## Bug Report ### Affected tool(s) or class(es) Mutect2 ### Affected version(s) 4.4.0.0 ### Description Hello GATK team, I am working on a pipeline that calls variants using Mutect2 and...

lculibrk

GenomicsDB malloc unaligned tcache chunk error

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---- ## Bug Report ### Affected tool(s) or class(es) - Tool/class name(s), special parameters: GenomicsDBImport ### Affected version(s) - Version: gatk4-4.4.0.0-0 ### Description Hello, I have been having an issue...

danagibbon

Remove hdfs support for GenomicsDB

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nalinigans

Docker image (broadinstitute/gatk) has too many unnecessary layers potentially causing throttling issues

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## Bug Report ### Affected tool(s) or class(es) The docker image: `broadinstitute/gatk` ### Affected version(s) `latest` ### Description - The current GATK image has 44 layers - In [the Azure...

MattMcL4475

Reverting the CombineGVCFs and GenotypeGVCFs to the old behavior for no-calls when there are no PLs present.

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Initial check-in to find test failures. Adresses #8328

jamesemery

GenotypeGVCFs: Add ability to convert current (0/0) genotype format to standard (./.) format

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## Feature request ### Tool(s) or class(es) involved *GenotypeGVCFs* as of GATK version 4.2.3.0 and newer. ### Description As of GATK version 4.2.3.0, *GenotypeGVCFs* began representing missing genotypes in the...

derekca

Refactoring a confusing method in GATKVariantContextUtils

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baking a null check into isInformative since it's always used with the check separating all cases out and reducing nesting of ifs

lbergelson

Updated Python and PyMC, removed TensorFlow, and added PyTorch in conda environment.

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Copying over some discussion from Slack, with some slight modifications: > I took a quick stab at updating the environment for gCNV. Even taking out TensorFlow (assuming that the CNN...

samuelklee

Combining aws-java-nio-spi-for-s3 with GATK.

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# Introduction Recently, Amazon has created the tool [aws-java-nio-spi-for-s3](https://github.com/awslabs/aws-java-nio-spi-for-s3) that allows java-based applications to read and/or write to aws without the need for recompilation during runtime. Since then, we've utilised...

DanishIntizar