broadinstitute/gatk 4.0.3.0

on GitHub

This release brings a major update to our experimental neural-network-based VariantRecalibrator replacement, initial MAF support in Funcotator, as well as some updates to Mutect2 and the CNV tools.

As usual, a docker image for this release can be downloaded from https://hub.docker.com/r/broadinstitute/gatk/

Summary of changes in this release:

• A major update to our experimental neural-network-based suite of variant scoring tools, which will eventually replace the VariantRecalibrator (#4245)

  • The NeuralNetInferenceTool has been renamed to CNNScoreVariants
  • Baseline models are now included in the distribution.
  • Added additional tools to write tensors and to train your own models given a VCF of validated calls, an unfiltered VCF and a confident region: CNNVariantTrain, CNNVariantWriteTensors and FilterVariantTranches
  • Read-level 2D models are now supported via the tensor-type read_tensor argument. 2D models at present are significantly slower than the 1D models.

• Funcotator:

  • Added prototype support for outputting MAF files (and many bug fixes) (#4472)

• Mutect2:

  • CalculateContamination emits its segmentation and Mutect2 germline model uses it (#4509)
  • Option to emit (but still filter) all germline sites in Mutect2 (#4522)
  • Made number of samples to put variant site in Mutect2 PON adjustable (#4566)
  • Added Oncotator filtering enabled in Mutect2 WDL. (#4423)

• CNV tools:

  • Replaced CollectFragmentCounts with CollectReadCounts. (#4564)
  • Allowed use of zero eigensamples in DenoiseReadCounts. (#4411)
  • Changed filtering of normal hets on overlap with copy-ratio intervals in ModelSegments to be consistent with filtering of case hets. (#4510)
  • Updated PostprocessGermlineCNVCalls (segments VCF writing, WDL scripts, unit tests, integration tests) (#4396)

• Miscellaneous changes:

  • Concordance: added option to analyze contributions of different filters (#4520)
  • Exposed the -pairHMM/--pair-hmm-implementation argument in HaplotypeCaller, which was previously hidden (#4494)
  • Set the default samjdk.compression_level to 2 (was previously 1) (#4547)
  • Upgraded to Spark 2.2.0 (#4314)
  • Changed Spark sharding of queryname-sorted bams to better handle secondary and supplementary reads (#4473)
  • Added logging output to the bam writing step for spark tools (#4501)
  • git-lfs is now required to compile the GATK
  • Added a registry for deprecated/unported tools. (#4505)
  • Updated the Hadoop GCS connector from 1.6.1 to 1.6.3. (#4590)
  • Added a large runtime resource directory to git-lfs, and exposed it to the Docker build. (#4530)
  • We now include full tool documentation in the GATK binary distribution zip (#4377)
  • Made our maven artifacts much smaller by preventing gradle uploadArchives from including distZip and distTar (#4569)
  • Added chr20 and chr21 alt contigs to the GRCh38 reference snippet used for testing (#4548)