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Release notes for GATK version 3.7

By Geraldine_VdAuwera

GATK 3.7 was released on December 12, 2016. Itemized changes are listed below. For more details, see the user-friendly version highlights.

HaplotypeCaller + GGVCFs

  • 39da22b - Changes to use the median rather than the second best likelihood for the NON_REF allele
  • a8797f2 - Fixed merging of GVCF blocks by fixing rounding of GQ values in ReferenceConfidenceModel
  • ce4ed1f - Remove NON_REF from allSites VCF output
  • ba21b22 - Do not emit GVCF block definitions in the header of the final VCF emitted by GenotypeGVCFs
  • 6670d12 - Changed maximum allowed GQB value to 100
  • e7bd143 - Added exception for GQB values greater than MAX_GENOTYPE_QUAL and tests
  • 9ae9b26 - Deprecate -stand_emit_conf
  • 04a70bb - Remove -stand_emit_conf argument
  • 5b8bf1c - Change default value of STANDARD_CONFIDENCE_FOR_CALLING to 10
  • a8db074 - Backport new AFCalculator
  • ad3e4f4 - Backport numerics changes in new qual
  • dc0fa3f - Fixes NaN issue in new Qual calculator


  • d7f1a9c - Lots of small improvements to Mutect2 code
  • 408d31d - More small refactorings of Mutect2 code
  • ff1e3a3 - Finish porting MuTect1 clustered read position filter
  • ce7d4bd - Port the strand bias filter from M1 and refactored code around SomaticGenotypingEngine; added a new integration test
  • 1350c0e - Add new annotator for M1 clustered read position filter and M1 strand bias filter
  • 095a469 - Cleaned up SomaticGenotypingEngine::callMutations and added some TODOs
  • e6d0318 - Expose downsampling arguments in Mutect

Allele prioritization and culling

  • a557ff3 - RCM Variant sites merger won't output PL when there are too many alleles in order to avoid memory issues with large cohort runs
  • 7296dbf - Remove alt alleles, when genotype count is explosively large, based on alleles' highest supporting haplotype score; max tolerable genotype count is controlled by a default value overridable by user
  • 5b09639 - Impose a maximum allele list message length
  • 7cd8a66 - Make sure that multi-allelic uninformative PLs (0,0,...,0) stay uninformative after biallelization
  • f182fc1 - Make alt allele removal by likelihoods robust to ref allele indices
  • 1709765 - Fixed a max priority Q error while removing alt alleles when faced with high ploidy and allele count

Misc annotations

  • 1f4fa57 - Change to max value of ExcessHet
  • 186d616 - Fix for int overflow in RankSum calculation
  • 5931311 - Remove RankSumTest and RMSAnnotation from hom-ref sites
  • 4c1365f - BaseCountsBySample counting bases at a particular position
  • f0874d1 - Bypass spanning deletions in Rank Sum tests
  • a327c24 - Makes Fisher's exact test match R and GATK4 results
  • 92a5aad - Fixed logic error and tidied AlleleBalance and AlleleBalanceBySample

Misc tools

  • 41c9fed - Add read group identifier to column names in ReadLengthDistribution
  • d96c02b - Allows GatherBqsrReports to accept a .list file as input
  • 22a3008 - SelectVariants works with non-diploids
  • 0dd96ac - Added TreeReduce interface to VariantFiltration
  • b85fea3 - Fix for genotype filters issue in VariantFiltration
  • 4341a2e - Assorted documentation fixes

Engine options

  • 69af359 - Added option to merge GenomeLocs that are abutting (contiguous) rather than actually overlapping
  • 541243b - Make interval padding work for "exclude intervals"
  • 4e4ac94 - Enable control of reporting periodicity
  • 68f1822 - Set HTSJDK log level
  • 359f078 - Throw an exception if the BQSR input covariates file is not found

Under the hood

  • 975c17a - Throw an exception for invalid Picard intervals
  • ce1d4c8 - Upgrade Apache Commons Collections to version 3.2.2
  • 355d053 - Move htsjdk and picard to version 2.5.0
  • 08b8eab - Move htsjdk to ver 2.6.1 and picard to ver 2.6.0
  • 4d45102 - Move htsjdk to ver 2.8.1 and picard to ver 2.7.2
  • f410451 - Change HashMap to LinkedHashMap for predictable ordering
  • 5fac5c8 - Added support for directly reading SRA runs
  • a5cc81a - Remove SRA group
  • 899453b - Write saved WARN messages to stderr instead of stdout
  • bed804d - Replace SAMFileReader with calls to SamReaderFactory
  • a48d36d - Assign correct ambiguity code for * allele
  • 496564f - Removed spanning deletions if the deletion was removed when subsetting
  • a37886f - Fix adapter boundary for positive strand in handling of overlapping read pairs
  • f6b18c8 - Fix issue where VCF files with "bcf" in the name were output to BCF
  • 4d6d207 - Replace VariantContextWriterFactory with VariantContextWriterBuilder
  • 6b8740e - Make exit system file type message generic


  • e6d34af - Make ReadPosRankSumTest.isUsableRead() account for deletions
  • e4786ed - Added regression test for genotyping of spanning deletions in GenotypeGCVFs
  • f709898 - Add integration test using -maxNumPLValues for GenotypeGVCFs
  • dfcec64 - Fix BetaTestingAnnotation group Add test
  • f7ff6b8 - Change a truth VCF in VQSR tests
  • d5ad2f0 - Make getElementForRead() in RankSumTest robust
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