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GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

# Release notes for GATK version 2.1

edited August 2012

## Base Quality Score Recalibration

• Multi-threaded support in the BaseRecalibrator tool has been temporarily suspended for performance reasons; we hope to have this fixed for the next release.
• Implemented support for SOLiD no call strategies other than throwing an exception.
• Fixed smoothing in the BQSR bins.
• Fixed plotting R script to be compatible with newer versions of R and ggplot2 library.

## Unified Genotyper

• Renamed the per-sample ML allelic fractions and counts so that they don't have the same name as the per-site INFO fields, and clarified the description in the VCF header.
• UG now makes use of base insertion and base deletion quality scores if they exist in the reads (output from BaseRecalibrator).
• Changed the -maxAlleles argument to -maxAltAlleles to make it more accurate.
• In pooled mode, if haplotypes cannot be created from given alleles when genotyping indels (e.g. too close to contig boundary, etc.) then do not try to genotype.
• Added improvements to indel calling in pooled mode: we compute per-read likelihoods in reference sample to determine whether a read is informative or not.

## Haplotype Caller

• Added LowQual filter to the output when appropriate.
• Added some support for calling on Reduced Reads. Note that this is still experimental and may not always work well.
• Now does a better job of capturing low frequency branches that are inside high frequency haplotypes.
• Updated VQSR to work with the MNP and symbolic variants that are coming out of the HaplotypeCaller.
• Made fixes to the likelihood based LD calculation for deciding when to combine consecutive events.
• Fixed bug where non-standard bases from the reference would cause errors.
• Better separation of arguments that are relevant to the Unified Genotyper but not the Haplotype Caller.

• Fixed bug where reads were soft-clipped beyond the limits of the contig and the tool was failing with a NoSuchElement exception.
• Fixed divide by zero bug when downsampler goes over regions where reads are all filtered out.
• Fixed a bug where downsampled reads were not being excluded from the read window, causing them to trail back and get caught by the sliding window exception.

## Variant Eval

• Fixed support in the AlleleCount stratification when using the MLEAC (it is now capped by the AN).
• Fixed incorrect allele counting in IndelSummary evaluation.

## Combine Variants

• Now outputs the first non-MISSING QUAL, instead of the maximum.
• Now supports multi-threaded running (with the -nt argument).

## Select Variants

• Fixed behavior of the --regenotype argument to do proper selecting (without losing any of the alternate alleles).
• No longer adds the DP INFO annotation if DP wasn't used in the input VCF.
• If MLEAC or MLEAF is present in the original VCF and the number of samples decreases, remove those annotations from the output VC (since they are no longer accurate).

## Miscellaneous

• GATK now generates a proper error when a gzipped FASTA is passed in.
• Various improvements throughout the BCF2-related code.
• Removed various parallelism bottlenecks in the GATK.
• Added support of X and = CIGAR operators to the GATK.
• Catch NumberFormatExceptions when parsing the VCF POS field.
• Fixed bug in FastaAlternateReferenceMaker when input VCF has overlapping deletions.
• Fixed AlignmentUtils bug for handling Ns in the CIGAR string.
• We now allow lower-case bases in the REF/ALT alleles of a VCF and upper-case them.
• Added support for handling complex events in ValidateVariants.
• Picard jar remains at version 1.67.1197.
• Tribble jar remains at version 110.
Post edited by rpoplin on

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

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