GATK 2.0On July 23rd, 2012, the Genome Sequencing and Analysis (GSA) team will release a beta of GATK 2.0. GATK 2.0 includes all of the original GATK 1.x tools as well as many newer and more advanced tools for error modeling, data compression, and variant calling:
- Base quality score recalibration (BQSR) v2, an upgrade to BQSR that generates a base substitution, insertion, and deletion error model.
- ReduceReads, 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.
- The HaplotypeCaller, a multi-sample local de novo assembly and integrated SNP, indel, and short SV caller.
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.
Mixed open/closed source model