GATK release 2.2 was released on October 31, 2012. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history

Base Quality Score Recalibration

  • Improved the algorithm around homopolymer runs to use a "delocalized context".
  • Massive performance improvements that allow these tools to run efficiently (and correctly) in multi-threaded mode.
  • Fixed bug where the tool failed for reads that begin with insertions.
  • Fixed bug in the scatter-gather functionality.
  • Added new argument to enable emission of the .pdf output file (see --plot_pdf_file).

Unified Genotyper

  • Massive runtime performance improvement for multi-allelic sites; -maxAltAlleles now defaults to 6.
  • The genotyper no longer emits the Stand Bias (SB) annotation by default. Use the --computeSLOD argument to enable it.
  • Added the ability to automatically down-sample out low grade contamination from the input bam files using the --contamination_fraction_to_filter argument; by default the value is set at 0.05 (5%).
  • Fixed annotations (AD, FS, DP) that were miscalculated when run on a Reduce Reads processed bam.
  • Fixed bug for the general ploidy model that occasionally caused it to choose the wrong allele when there are multiple possible alleles to choose from.
  • Fixed bug where the inbreeding coefficient was computed at monomorphic sites.
  • Fixed edge case bug where we could abort prematurely in the special case of multiple polymorphic alleles and samples with drastically different coverage.
  • Fixed bug in the general ploidy model where it wasn't counting errors in insertions correctly.
  • The FisherStrand annotation is now computed both with and without filtering low-qual bases (we compute both p-values and take the maximum one - i.e. least significant).
  • Fixed annotations (particularly AD) for indel calls; previous versions didn't accurately bin reads into the reference or alternate sets correctly.
  • Generalized ploidy model now handles reference calls correctly.

Haplotype Caller

  • Massive runtime performance improvement for multi-allelic sites; -maxAltAlleles now defaults to 6.
  • Massive runtime performance improvement to the HMM code which underlies the likelihood model of the HaplotypeCaller.
  • Added the ability to automatically down-sample out low grade contamination from the input bam files using the --contamination_fraction_to_filter argument; by default the value is set at 0.05 (5%).
  • Now requires at least 10 samples to merge variants into complex events.

Variant Annotator

  • Fixed annotations for indel calls; previous versions either didn't compute the annotations at all or did so incorrectly for many of them.

Reduce Reads

  • Fixed several bugs where certain reads were either dropped (fully or partially) or registered as occurring at the wrong genomic location.
  • Fixed bugs where in rare cases N bases were chosen as consensus over legitimate A,C,G, or T bases.
  • Significant runtime performance optimizations; the average runtime for a single exome file is now just over 2 hours.

Variant Filtration

  • Fixed a bug where DP couldn't be filtered from the FORMAT field, only from the INFO field.

Variant Eval

  • AlleleCount stratification now supports records with ploidy other than 2.

Combine Variants

  • Fixed bug where the AD field was not handled properly. We now strip the AD field out whenever the alleles change in the combined file.
  • Now outputs the first non-missing QUAL, not the maximum.

Select Variants

  • Fixed bug where the AD field was not handled properly. We now strip the AD field out whenever the alleles change in the combined file.
  • Removed the -number argument because it gave biased results.

Validate Variants

  • Added option to selectively choose particular strict validation options.
  • Fixed bug where mixed genotypes (e.g. ./1) would incorrectly fail.
  • improved the error message around unused ALT alleles.

Somatic Indel Detector

  • Fixed several bugs, including missing AD/DP header lines and putting annotations in correct order (Ref/Alt).

Miscellaneous

  • New CPU "nano" parallelization option (-nct) added GATK-wide (see docs for more details about this cool new feature that allows parallelization even for Read Walkers).
  • Fixed raw HapMap file conversion bug in VariantsToVCF.
  • Added GATK-wide command line argument (-maxRuntime) to control the maximum runtime allowed for the GATK.
  • Fixed bug in GenotypeAndValidate where it couldn't handle both SNPs and indels.
  • Fixed bug where VariantsToTable did not handle lists and nested arrays correctly.
  • Fixed bug in BCF2 writer for case where all genotypes are missing.
  • Fixed bug in DiagnoseTargets when intervals with zero coverage were present.
  • Fixed bug in Phase By Transmission when there are no likelihoods present.
  • Fixed bug in fasta .fai generation.
  • Updated and improved version of the BadCigar read filter.
  • Picard jar remains at version 1.67.1197.
  • Tribble jar remains at version 110.

brdido


Hello, we've noticed that DP in VCF field FORMAT was missing in our VCFs using Haplotype Caller in GATK version 2.5-2-gf57256b , but it still exists in the header: ##FORMAT= FORMAT GT:AD:GQ:PL I'm commenting here because i found some bug fixes in this release note regarding this issue. Could someone help me check if those problems are back in v2.5 ? Thanks

Wed 31 Oct 2012

Geraldine_VdAuwera


I think what you're referring to (the SomaticIndelDetector bug fix?) was a different issue. Are you saying that the DP annotation is missing entirely from the vcf produced by the HC, or that the name DP is missing from the format field "legend", while the value is present?

Wed 31 Oct 2012




At a glance


Follow us on Twitter

GATK Dev Team

@gatk_dev

RT @kasper_lage: Public service announcement: @gaddyg account is showing a pulse again. All interested in cancer, genetics & science should…
30 Apr 16
@embatty @BrockhurstLab @conTAMInatedsci @alanmcn1 Unfortunately some code flaws cause >20+ ploidy to be v. slow. On to-fix list.
28 Apr 16
Right! And +1M back at you on being more specific about *which* technology/platform. #ngsmustdie https://t.co/440d1Kybte
27 Apr 16
@MrsLaviniaG Having a distinguishing term is indeed useful. Point is it should be a meaningful term. Next-gen is no longer meaningful.
27 Apr 16
@BenNMiles Phones still smart(er) whereas NGS is based on past state. Collision w/ screening is real; but context disambiguates?
27 Apr 16

Our favorite tweets from others

@gatk_dev Hey guys thanks for another fantastic workshop, hope you all had a good time in the pub. I’m now back the other side of the wall
14 Apr 16
@gatk_dev @notSoJunkDNA The cloud giveth, the cloud taketh
6 Apr 16
.@gatk_dev The genotype likelihood blog post is very nice. Thank you! https://t.co/ZFPiZVaoKe via @bricesarver
23 Mar 16
@gatk_dev thanks, will certainly have a look over WDL + Cromwell. Also like the memes on front page!
18 Mar 16
Great to learn about GATK at the GATK workshop at @UCLA. Thanks @gatk_dev team!
2 Mar 16
See more of our favorite tweets...
Search blog by tag

ad appistry ashg benchmarks best-practices bug bug-fixed cancer catvariants challenge cloud cluster combinegvcfs commandline commandlinegatk competition compute conferences cram cromwell denovo depthofcoverage diagnosetargets error fastaalternatereferencemaker fix forum gatk3 genotype genotype-refinement genotypegvcfs google gvcf haploid haplotypecaller hardware holiday hts htsjdk ibm job job-offer jobs joint-analysis joint-discovery key license media meetings mendelianviolations multisample multithreading mutect mutect2 ngs nt outreach pairhmm paper parallelism patch performance phone-home picard pipeline plans ploidy polyploid poster presentations press printreads profile promote randomlysplitvariants readbackedphasing reducereads reference-model release release-notes rnaseq runtime saas search selectvariants sequencing service slides snow speed splitncigarreads status sting support syntax talks team terminology third-party-tools topstory trivia troll tutorial unifiedgenotyper variantannotator variantrecalibrator version-highlights versions video vqsr wdl webinar workflow workshop