broadinstitute/gatk 4.beta.2

on GitHub

This is a bug fix release primarily aimed at fixing some issues in the Mutect2 WDL. The major known issues listed in the release notes for 4.beta.1 still apply.

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.

Changes in this release:

• Mutect2 WDL: corrected the ordering of FilterMutectCalls relative to FilterByOrientationBias. FilterByOrientationBias should always be run after all other filters, since (by design) it is trying to keep a bound on the FDR rate. See issue #3288
• Mutect2 WDL: added automated extraction of bam sample names from the input bam files, using samtools. This should be viewed as a temporary fix until named parameters are in place. See issue #3265
• FilterByOrientationBias: fixed to no longer throw IllegalStateExceptions when running on a large number of variants. This was due to a hashing collision in a sorted map. See issue #3291.
• FilterByOrientationBias: non-diploid warnings have been set to debug severity. This should reduce the stdout. As a side-effect, this should address/attenuate a comment in issue #3291.
• VcfToIntervalList: added ability to generate interval list on all variants, not just the ones that passed filtering. Please note that this change may need to be ported to Picard. Added an automated test that should fail if this mechanism is broken in the GATK. See PR #3250
• CollectAllelicCounts: now inherits from LocusWalker, rather than custom traversal. This reduced the amount of code. See issue #2968 (and PR #3203 for some other changes)
• Added experimental (and unsupported) tool CalculatePulldownPhasePosteriors at a user request. See issue #3296
• Implement PathSeqScoreSpark and PathSeqBwaSpark tools, and update PathSeqFilterSpark and PathSeqBuildKmers tools
• Many changes to Mutect2 Hapmap validation WDL
• GatherVcfs: support block copy mode with GCS inputs
• GatherVcfs: fix crash when gathering files with no variants
• AlleleSubsettingUtils: if null likelihoods, don't add to likelihoods sums (fixes #3210)
• SV tools: add small indel evidence
• SV tools: several FASTQ-related fixes (#3131, #2754, #3214)
• SV tools: always use upstream read when looking at template lengths
• SV tools: fix bugs in the SV pipeline's cross-contig ignore logic regarding non-primary contigs
• SV tools: switch to dataproc image 1.1 in create_cluster.sh
• SV tools: FindBreakEvidenceSpark can now produce a coordinate sorted Assemblies bam
• Bait count bias correction for TargetCoverageSexGenotyper
• CountFalsePositives: fix so it a) does not return garbage for target territory and b) returns a proper fraction for false positive rate
• Specify UTF-8 encoding in implementations of GATKRead.getAttributeAsByteArray()
• GATK engine: fix sort order when reading multiple bams
• Fix GATKSAMRecordToGATKReadAdapter.getAttributeAsString() for byte[] attributes
• Fix various issues that were causing Travis CI test suite runs to fail intermittently