GATK 3.3 was released on October 23, 2014. Itemized changes are listed below. For more details, see the user-friendly version highlights.


Haplotype Caller

  • Improved the accuracy of dangling head merging in the HC assembler (now enabled by default).
  • Physical phasing information is output by default in new sample-level PID and PGT tags.
  • Added the --sample_name argument. This is a shortcut for people who have multi-sample BAMs but would like to use -ERC GVCF mode with a particular one of those samples.
  • Support added for generalized ploidy. The global ploidy is specified with the -ploidy argument.
  • Fixed IndexOutOfBounds error associated with tail merging.

Variant Recalibrator

  • New --ignore_all_filters option. If specified, the variant recalibrator will ignore all input filters and treat sites as unfiltered.

GenotypeGVCFs

  • Support added for generalized ploidy. The global ploidy is specified with the -ploidy argument.
  • Bug fix for the case when we assumed ADs were in the same order if the number of alleles matched.
  • Changed the default GVCF GQ Bands from 5,20,60 to be 1..60 by 1s, 60...90 by 10s and 99 in order to give finer resolution.
  • Bug fix in the exact model when calling multi-allelic variants. QUAL field is now more accurate.

RNAseq analysis

  • Bug fixes for working with unmapped reads.

CalculateGenotypePosteriors

  • New annotation for low- and high-confidence possible de novos (only annotates biallelics).
  • FamilyLikelihoodsUtils now add joint likelihood and joint posterior annotations.
  • Restricted population priors based on discovered allele count to be valid for 10 or more samples.

DepthOfCoverage

  • Fixed rare bug triggered by hash collision between sample names.

SelectVariants

  • Updated the --keepOriginalAC functionality in SelectVariants to work for sites that lose alleles in the selection.

PrintReads

  • Read groups that are excluded by sample_name, platform, or read_group arguments no longer appear in the header.
  • The performance penalty associated with filtering by read group has been essentially eliminated.

Annotations

  • StrandOddsRatio is now a standard annotation that is output by default.
  • We used to output zero for FS if there was no data available at a site, now we omit FS.
  • Extensive rewrite of the annotation documentation.

Queue

  • Fixed Queue bug with bad localhost addresses.
  • Fixed issue related to spaces in job names that were fine in GridEngine 6 but break in (Son of) GE8.
  • Improved scatter contigs algorithm to be fairer when splitting many contigs into few parts (contributed by @smowton)

Documentation

  • We now generate PHP files instead of HTML.
  • We now output a JSON version of the tool documentation that can be used to generate wrappers for GATK commands.

Miscellaneous

  • Output arguments --no_cmdline_in_header, --sites_only, and --bcf for VCF files, and --bam_compression, --simplifyBAM, --disable_bam_indexing, and --generate_md5 for BAM files moved to the engine level.
  • htsjdk updated to version 1.120.1620

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tommycarstensen on 23 Oct 2014


> @Geraldine_VdAuwera said: > ##Documentation > - We now output a JSON version of the tool documentation that can be used to generate wrappers for GATK commands. This sounds cool. Is there an example somewhere?

Geraldine_VdAuwera on 23 Oct 2014


They're all available online -- if you go to the tool docs, for every tool page you can just switch out the ".php" extension with ".json", and voila!




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