broadinstitute/gatk 4.beta.3

on GitHub

This release contains a number of bug fixes and improvements. Highlights include a fix for intermittent failures/timeouts when accessing data in Google Cloud Storage (GCS), new and improved active-region detection for Mutect2, and a new VariantRecalibrator argument to allow the tool to scale better. See the full list of changes below. Most of the major known issues listed in the release notes for 4.beta.1 still apply, with the exception of the "intermittent GCS failures/timeouts" issue, which is now resolved.

A docker image for this release can be found in the broadinstitute/gatk repository on dockerhub. Within the image, cd into /gatk then run gatk-launch commands as usual.

Note: Due to our current dependency on a snapshot of google-cloud-java, this release cannot be published to maven central.

Changes in this release:

• GATK engine: Move to google-cloud-java snapshot with more robust retries, and set number of retries/reopens globally. This fixes the intermittent "all retries/reopens failed" error when accessing data on GCS (Google Cloud Storage). See issue #2749
• Mutect2: Implemented a new algorithm for active-region detection, reducing spurious active regions by almost 50%
• Mutect2: Filter artifacts that arise from apparent-duplicate reads
• Mutect2 WDL: Oncotator is now being told the case and control sample names explicitly in the WDL. The Oncotator code for inferring this could yield incorrect answers in some cases. See issue #3343
• FilterByOrientationBias: We discovered that it is impossible to guarantee a FDR threshold of all the variants when one artifact mode had high oxoQ and the other had low. We have changed the tool to guarantee the FDR threshold within each artifact mode, rather than for all variants. For more details, see issue #3344
• FilterByOrientationBias: Summary table was not being populated properly. That has been fixed. See issue #3309
• VariantRecalibrator: Add argument to pre-sample data for VQSR model building (and also recalibration) to reduce memory usage for production pipeline. See issue #3230
• Fix a stack overflow issue at high depths in the strand artifact annotation. See issue #3317
• GenomicsDBImport: add --readerThreads argument for multi-threaded vcf pre-loading. Improves performance of the tool by ~30% in our tests.
• ValidateVariants: port gvcf validation option from GATK3
• Polish up PathSeq and add pipeline tool
• Fix error message describing how to set the GATK_STACKTRACE_ON_USER_EXCEPTION property
• Mutect2FilteringEngine: correct MEDIAN_BASE_QUALITY_DIFFERENCE_FILTER and MEDIAN_MAPPING_QUALITY_DIFFERENCE_FILTER filter names
• Mutect2 WDL: gave ProcessOptionalArguments a leaner docker
• GATK4 Docker Image: changed the landing directory for the docker image to be /gatk instead of /root
• Travis CI: fixed test report not being uploaded to GCS
• Travis CI: removed non-docker unit and integration tests, which were redundant