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# Release notes for GATK version 2.0

Broad InstituteMember, Administrator, Broadie, Moderator, Dev Posts: 692 admin
edited August 2012

The GATK 2.0 release includes both the addition of brand-new (and often still experimental) tools and updates to the existing stable tools.

## New Tools

• Base Recalibrator (BQSR v2), an upgrade to CountCovariates/TableRecalibration that generates base substitution, insertion, and deletion error models.
• Reduce Reads, a BAM compression algorithm that reduces file sizes by 20x-100x while preserving all information necessary for accurate SNP and indel calling. ReduceReads enables the GATK to call tens of thousands of deeply sequenced NGS samples simultaneously.
• HaplotypeCaller, a multi-sample local de novo assembly and integrated SNP, indel, and short SV caller.
• Plus powerful extensions to the Unified Genotyper to support variant calling of pooled samples, mitochondrial DNA, and non-diploid organisms. Additionally, the extended Unified Genotyper introduces a novel error modeling approach that uses a reference sample to build a site-specific error model for SNPs and indels that vastly improves calling accuracy.

## Base Quality Score Recalibration

• IMPORTANT: the Count Covariates and Table Recalibration tools (which comprise BQSRv1) have been retired! Please see the BaseRecalibrator tool (BQSRv2) for running recalibration with GATK 2.0.

## Unified Genotyper

• Handle exception generated when non-standard reference bases are present in the fasta.
• Bug fix for indels: when checking the limits of a read to clip, it wasn't considering reads that may already have been clipped before.
• Now emits the MLE AC and AF in the INFO field.
• Don't allow N's in insertions when discovering indels.

## Phase By Transmission

• Multi-allelic sites are now correctly ignored.
• Reporting of mendelian violations is enhanced.
• Corrected TP overflow.
• Fixed bug that arose when no PLs were present.
• Added option to output the father's allele first in phased child haplotypes.
• Fixed a bug that caused the wrong phasing of child/father pairs.

## Variant Eval

• Improvements to the validation report module: if eval has genotypes and comp has genotypes, then subset the genotypes of comp down to the samples being evaluated when considering TP, FP, FN, TN status.
• If present, the AlleleCount stratification uses the MLE AC by default (and otherwise drops down to use the greedy AC).
• Fixed bugs in the VariantType and IndelSize stratifications.

## Variant Annotator

• FisherStrand annotation no longer hard-codes in filters for bases/reads (previously used MAPQ > 20 && QUAL > 20).
• Miscellaneous bug fixes to experimental annotations.
• Added a Clipping Rank Sum Test to detect when variants are present on reads with differential clipping.
• Fixed the ReadPos Rank Sum Test annotation so that it no longer uses the un-hardclipped start as the alignment start.
• Fixed bug in the NBaseCount annotation module.
• The new TandemRepeatAnnotator is now a standard annotation while HRun has been retired.
• Added PED support for the Inbreeding Coefficient annotation.
• Don't compute QD if there is no QUAL.

## Variant Quality Score Recalibration

• The VCF index is now created automatically for the recalFile.

## Variant Filtration

• Now allows you to run with type unsafe JEXL selects, which all default to false when matching.

## Select Variants

• Added an option which allows the user to re-genotype through the exact AF calculation model (if PLs are present) in order to recalculate the QUAL and genotypes.

## Combine Variants

• Added --mergeInfoWithMaxAC argument to keep info fields from the input with the highest AC value.

## Somatic Indel Detector

• GT header line is now output.

## Indel Realigner

• Automatically skips Ion reads just like it does with 454 reads.

## Variants To Table

• Genotype-level fields can now be specified.
• Added the --moltenize argument to produce molten output of the data.

## Depth Of Coverage

• Fixed a NullPointerException that could occur if the user requested an interval summary but never provided a -L argument.

## Miscellaneous

• BCF2 support in tools that output VCFs (use the .bcf extension).
• The GATK Engine no longer automatically strips the suffix "Walker" after the end of tool names; as such, all tools whose name ended with "Walker" have been renamed without that suffix.
• Fixed bug when specifying a JEXL expression for a field that doesn't exist: we now treat the whole expression as false (whereas we were rethrowing the JEXL exception previously).
• There is now a global --interval_padding argument that specifies how many basepairs to add to each of the intervals provided with -L (on both ends).
• Removed all code associated with extended events.
• Algorithmically faster version of DiffEngine.
• Better down-sampling fixes edge case conditions that used to be handled poorly. Read Walkers can now use down-sampling.
• GQ is now emitted as an int, not a float.
• Fixed bug in the Beagle codec that was skipping the first line of the file when decoding.
• Fixed bug in the VCF writer in the case where there are no genotypes for a record but there are genotypes in the header.
• Miscellaneous fixes to the VCF headers being produced.
• Fixed up the BadCigar read filter.
• Removed the old deprecated genotyping framework revolving around the misordering of alleles.
• Extensive refactoring of the GATKReports.
• Picard jar updated to version 1.67.1197.
• Tribble jar updated to version 110.
Post edited by Geraldine_VdAuwera on

Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

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