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

Return to top

Comment on this article

- Recent posts

- Upcoming events

See Events calendar for full list and dates

- Recent events

See Events calendar for full list and dates

- Follow us on Twitter

GATK Dev Team


@FanBoyShi For this kind of question we'd prefer you post in the forum so we can troubleshoot in detail -- but if…
8 Dec 19
RT @seandavis12: Calling Somatic SNVs and Indels with Mutect2
3 Dec 19
Couldn’t have said it better
3 Dec 19
RT @broadinstitute: Genome sequencing technology allows for massive amounts of high-quality data to be produced. Researchers at Broad have…
27 Nov 19
Heads up: we’re moving the GATK website, docs and forum to a new platform. Full story and breakdown of key changes…
21 Nov 19

- Our favorite tweets from others

@CBIB_UNAB @gatk_dev @TerraBioApp This project is the product of ongoing collaborations with @SGWilliams1980 and…
28 Oct 19
Si estas en #SOIBIO+10, acércate del poster 48! I will be talking about my latest research at @CBIB_UNAB looking i…
28 Oct 19
After the Gatk workshop, I can only say thanks to @gatk_dev and @broadinstitute for their great effort to create a…
25 Oct 19
Hoy termina el GATK Workshop que nuestra Área de Bioinformática Clínica ha organizado en el centro de simulación cl…
25 Oct 19

See more of our favorite tweets...