2.7.0

Updated workflow to {GATK4.1.4.1](https://github.com/broadinstitute/gatk/releases/tag/4.1.4.1)

• Mutect2 now warns but does not fail when three or more reads have the same name. (#6240)
• Fixed the random seed at the beginning of FilterMutectCalls (#6208)
• GetSampleName and GetPileupSummaries in the M2 pipeline are no longer beta. (#6215)
• Increase number of iterations in CalculateContamination to 30. (#6282)
• Handled an edge case with high scatter count in M2 WDL. (#6216)
• Use ArgumentsBuilder in M2 tests. (#6219)

2.6.0

Update WDL to GATK 4.1.4.0 release.

• WDL now written in WDL 1.0 -- enabling call-caching on Terra
• Oncotator is no longer an option -- the workflow only supports Functotator now

2.5.0

• Updated to GATK4.1.2.0 - Release Notes Here

2.4.0

• Updated to GATK4.1.1.0 - Release Notes Here

2.3.0

Updated to GATK4.1 release.
Updated import to Git release tag URLs

2.2.0

• Update to gatk4.0.8.1 docker
• Added link to 'How to run workflow' document

2.1.0

• Updated for gatk4.0.5.0. Scripts uses files from master that are slightly further in commits but will still work with this release.
• The new output maf_segments should be hooked up to this.maf_segments for pair workflows.
• Added new input realignment_index_bundle, needs further test before being a default. Users can access the resource file from the following google bucket : gs://gatk-test-data/mutect2/Homo_sapiens_assembly38.index_bundle

Mutect2 2.0.0

• Update to gatk4.0.4.0
• Handle sample names with spaces correctly
• Pass VCF indices correctly
• Added mutect2_pon.wdl and json. Publicly available normal bams are not available, thus the provided json has not defined inputs for testing.
• Added Parameter Description in Readme
• Addition of mutect2 validation workflow
• Added NIO enabled wdl
• WDL updates include a couple of minor bug fixes
• A new "given alleles" mode where the user can input a vcf of variants that Mutect2 is forced to genotype, regardless of how little evidence there may be.
• Update oncotator docker image

Mutect2 based on Gatk4.0.1.1

Updated to gatk4.0.1.1 release

• Picard tools are called from the GATK, so you no longer need to input a picard jar.
• No longer need to input the path to the gatk in the docker image.
• Ability to run Funcotator.
• Ability to produce a bamout.
• Ability to compress vcf output.
• The wdl now works with cram inputs.
• The contamination tool uses the matched normal when it can.
• The contamination variants input can be a compressed vcf.

GATK4 MuTect2 workflow (beta)

This is the initial release of the GATK4 MuTect2 workflow for somatic SNV and Indel discovery developed by the GATK team at the Broad Institute. It includes the core workflow WDL, a JSON of inputs for the exome use case, and a JSON of generic options for running via Cromwell on the Google Pipelines API (PAPI).

Requirements

The workflow was tested with GATK version 4.beta.3 and is expected to work with versions up to 4.beta.5 (current version at time of release). It should be runnable on any platform that supports WDL. The included JSON points to data files hosted on the Google Cloud Storage platform.