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 on 31 Oct 2012


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

Geraldine_VdAuwera on 31 Oct 2012


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?




- 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

@gatk_dev

Services are coming back online gradually thanks to the tireless efforts of the @broadinstitute IT ops team. #GATK… https://t.co/Fb4DWcqoQM
24 Jun 18
@KaeKogane Yes, there was a fire that brought down power systems in our data center. Our operations team is still w… https://t.co/iW14DuszNj
23 Jun 18
Service notice: the #GATK website is down due to a data center fire. The support forum remains functional, and most… https://t.co/uWsp11FOa8
23 Jun 18
RT @BroadFireCloud: Heads up folks: https://t.co/AQzNTDmCoj is not available due to a local data center fire. https://t.co/11tQWPNJFq may b…
23 Jun 18
@geoffjentry @nilshomer Willing to provide emotional support (no geographic limitations)
21 Jun 18

- Our favorite tweets from others

Important thread. Using ExAC or gnomAD as “convenience controls” in association studies is a very dangerous game, w… https://t.co/MTlCGF6vXH
22 Jun 18
Performance benchmarking of GATK3.8 and GATK4 https://t.co/SclOTAi6We (Spoiler: GATK4's significantly faster) by… https://t.co/aI9U0Tu5Q6
19 Jun 18
Weronika Gutowska-Ding: In the EMQN NGS rounds, BWA and GATK the most used aligner and variant caller. Variant call… https://t.co/oLTwUWpo9L
16 Jun 18
Thank you to @broadinstitute & @geoffjentry and their amazing software engineering team for hosting my talk today.… https://t.co/XIR7Fx1nOJ
11 Jun 18
Congrats! It’s great to see @WDL_dev getting stronger adoption for portable workflows in the bioinformatics communi… https://t.co/xZqjxgzDCK
5 Jun 18

See more of our favorite tweets...