Release notes for GATK version 2.3

ebanks

GATK 2.3 was released on December 17, 2012. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history

Base Quality Score Recalibration

• Soft clipped bases are no longer counted in the delocalized BQSR.
• The user can now set the maximum allowable cycle with the --maximum_cycle_value argument.

Unified Genotyper

• Minor (5%) run time improvements to the Unified Genotyper.
• Fixed bug for the indel model that occurred when long reads (e.g. Sanger) in a pileup led to a read starting after the haplotype.
• Fixed bug in the exact AF calculation where log10pNonRefByAllele should really be log10pRefByAllele.

Haplotype Caller

• Fixed the performance of GENOTYPE_GIVEN_ALLELES mode, which often produced incorrect output when passed complex events.
• Fixed the interaction with the allele biased downsampling (for contamination removal) so that the removed reads are not used for downstream annotations.
• Implemented minor (5-10%) run time improvements to the Haplotype Caller.
• Fixed the logic for determining active regions, which was a bit broken when intervals were used in the system.

Variant Annotator

• The FisherStrand annotation ignores reduced reads (because they are always on the forward strand).
• Can now be run multi-threaded with -nt argument.

Reduce Reads

• Fixed bug where sometime the start position of a reduced read was less than 1.
• ReduceReads now co-reduces bams if they're passed in toghether with multiple -I.

Combine Variants

• Fixed the case where the PRIORITIZE option is used but no priority list is given.

Phase By Transmission

• Fixed bug where the AD wasn't being printed correctly in the MV output file.

Miscellaneous

• A brand new version of the per site down-sampling functionality has been implemented that works much, much better than the previous version.
• More efficient initial file seeking at the beginning of the GATK traversal.
• Fixed the compression of VCF.gz where the output was too big because of unnecessary call to flush().
• The allele biased downsampling (for contamination removal) has been rewritten to be smarter; also, it no longer aborts if there's a reduced read in the pileup.
• Added a major performance improvement to the GATK engine that stemmed from a problem with the NanoSchedule timing code.
• Added checking in the GATK for mis-encoded quality scores.
• Fixed downsampling in the ReadBackedPileup class.
• Fixed the parsing of genome locations that contain colons in the contig names (which is allowed by the spec).
• Made ID an allowable INFO field key in our VCF parsing.
• Multi-threaded VCF to BCF writing no longer produces an invalid intermediate file that fails on merging.
• Picard jar remains at version 1.67.1197.
• Tribble jar updated to version 119.

severin

In the new release for the HaplotypeCaller function does downsampling do anything?
Can we still use --enable_experimental_downsampling?

What is your recommendation.

Geraldine_VdAuwera

You no longer need to use --enable_experimental_downsampling for anything; the experimental downsampling is now the regular downsampling (see Version history/Version highlights for details) and is used by default by all tools that downsample reads.