broadinstitute/gatk 4.0.12.0

on GitHub

Highlights of this release include support for outputting phased variants in HaplotypeCaller/Mutect2, restoring the --include-non-variant-sites argument to GenotypeGVCFs, a port of the GATK3 tool VariantEval, a new library (Disq, https://github.com/disq-bio/disq) for working with BAM/CRAM/VCF/etc. formats on Spark, and GCS (Google Cloud Storage) support in Funcotator.

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

Full list of changes in this release:

• HaplotypeCaller/Mutect2

  • Output VCF spec-compliant phased variants in HaplotypeCaller and Mutect2
  • Added an experimental adaptive pruning option for local assembly (#5473)
  • Improved implementation of allele-specific new qual (#5460)
  • Use cigar complexity to break ties in uninformative reads' best haplotypes (#5359)
  • Improved handling of regions that are too short after trimming in HaplotypeCaller and in Mutect2 (Closes issue #5079)
  • Optimization in CigarUtils to shortcut to M-only CIGAR when provably optimal (#5466)
  • Changed SUPPORTED_ALLELES_TAG from SA to XA (#5418)

• HaplotypeCaller

  • Fixed bug in GGA mode caused by split multallic sites with genotypes (#5365)
  • The debug command line argument is now passed correctly in HaplotypeCaller (fixed issue #4943) (#5455)

• Mutect2

  • Big improvements to CalculateContamination's model for determining hom alt sites (#5413)
  • Reduce false negatives from mapping quality filter on long indels in Mutect2 (#5497)
  • Added a mismatch ratio option in realignment filter (#5501)
  • Made Mutect2 read position filter default much less stringent (#5487)
  • Fixed M2 bug for germline resources with AF=. (#5442)
  • Fix read position annotation bug in M2 filter (#5495)
  • Cleaner Mutect2 VCF fields (#5510)
  • Moved PerAlleleAnnotations to the INFO field (#5518)
  • Removed unnecessary inheritance of M2 filtering arguments collection (#5498)

• GenotypeGVCFs

  • Restored the --include-non-variant-sites argument from GATK3 to GenotypeGVCFs (#5219)

• Ported the GATK3 tool VariantEval to GATK4 (#5043)

• Replaced the Hadoop-BAM library with the newly-developed Disq library (https://github.com/disq-bio/disq) for efficiently working with BAM/CRAM/VCF/etc. formats on Spark (#5138)

  • Improves Spark performance across-the-board, and fixes many edge-case bugs in Hadoop-BAM

• Funcotator

  • Added GCS support to Funcotator data sources, so that data sources can now be accessed directly from GCS buckets (#5425)
  • Added support for annotating 5'/3' flanks (#5403)
  • Funcotator now creates default annotations for difficult variants. (#5374)
  • Funcotator now can create annotations for symbollic alleles and masked alleles (#5406)
  • Funcotator now can match between hg19 and b37 data sources. (#5491)
  • Added in regression tests and fixes for correctness of many annotations (#5302)
  • Now DE_NOVO_START_IN_FRAME and DE_NOVO_START_OUT_FRAME are correct. (#5357)
  • Added cDNA Strings for Intronic Variants (#5321)
  • VCF data sources create an ID field for the ID of the variant
    used for the annotation (#5327)
  • Funcotator now computes MT protein changes. (#5361)
  • Funcotator now correctly populates transcript position. (#5380)
  • Added a script that can create data sources from BED files. (#5438)
  • Updated testing Gencode data sources to fully exercise test data set (#5423)
  • Moved validation test data out of large files area. (#5381)
  • Updated top-level class documentation for Funcotator. (#4655)
  • Added scripts to liftover gnomAD. Also bugfixes for Funcotator NIO. (#5514)

• HaplotypeCallerSpark

  • Added a "strict mode" that allows HaplotypeCallerSpark to closely match the output of the regular HaplotypeCaller (#5416)
  • Now extends AssemblyRegionWalkerSpark (#5386)

• MarkDuplicatesSpark: Added a few of the remaining unimplemented useful features from Picard (#5377)

• CNV workflows

  • Changed FilterIntervals to operate on the intersection of intervals in all inputs. (#5408)
  • Fixed RAM usage parameter error in combine_tracks.wdl (#5358)
  • Various other improvements to combine_tracks.wdl (#5384)
  • Fixed gCNV WDL broken by Cromwell update on FireCloud. (#5407)
  • Replaced bash script in gCNV ScatterIntervals task with updated version of IntervalListTools. (#5414)

• CNNScoreVariants

  • Check for and require hardware AVX support (#5291)

• Changed SelectVariants so that it can handle multiple rsIDs separated by ';' in a VCF file (#5464)

• Miscellaneous Changes

  • Added setIsUnplaced() to the GATKRead API to distinguish reads with no mapping information (#5320)
  • Fixed an integer overflow bug in the RMSMappingQuality annotation (#5435)
  • Fixed floating-point bug in MannWhitneyU on some JVMs. (#5371)
  • Standardized the output argument for LeftAlignIndels (#5474)
  • SplitIntervals now produces an .interval_list file (#5392)
  • Fixed a bug with GATK_GCS_STAGING in the GATK launcher script #1338 (#5452)
  • Added ExampleReadWalkerWithVariantsSpark.java and tests (#5289)
  • Add description getter and javadoc in GATKReportTable (#5443)
  • Fixed message in GATKAnnotationPluginDescription (#5444)
  • Replaced some uses of PrintWriter (#5461)
  • Refactor GVCFWriter to allow push/pull iteration. (#5311)
  • Add scripts/dataproc-cluster-ui to release bundle. (#5401)
  • Marked VariantAnnotator as a @DocumentedFeature (#5480)
  • Removed obsolete intel conda environment references. (#5482)
  • Deleted the CountSet class (#5467)
  • Test framework: disabled gcloud login on travis for non-cloud non-wdl tests (#5335)
  • Updated Spark scripts to reflect changes from #5386 and #5127. (#5415)
  • Fixed jexl logging and updated VariantFiltration doc. (#5422)
  • Fixed some dead links in the README (#5405)

• Dependencies

  • Updated htsjdk to 2.18.1 (#5486)
  • Updated Picard to 2.18.16. (#5412)
  • Updated Intel-GKL dependency to 8.6 (#5463)