The latest GATK release is out, with changes corresponding to the period of June 20, 2020 - October 10, 2020. The full GATK release notes are available on the GATK GitHub, but here is just a taste of what's new in GATK 126.96.36.199:
- There are two new tools available:
GeneExpressionEvaluationfor evaluating gene expression from RNA-seq reads aligned to the genome, and
ReferenceBlockConcordancefor evaluating the concordance of reference blocks in GVCF files.
This GATK update brings
Funcotatorup to the latest Gencode release, and fixes contig naming issues with dbSNP (leading to errors such as, for example, "hg38 dbSNP has incorrect contig names"). It also supports new tags, including the TAGENE gene tag and MANE_SELECT.
Fixed an issue with
FuncotateSegmentswhere the default value of
--alias-to-key-mappingwas being set to an immutable value.
Removed slow string formatting calls from
DepthOfCoverage, leading to significant performance improvements. In a locally run test, using default arguments, the runtime for a full chr15 WGS dropped from 8.9 min to 4.7 min.
- Significantly improved performance of
SelectVariantswith large numbers of samples. In a test run with several thousand samples, the runtime dropped from 5 minutes to 6 seconds.
- This update includes important bug fixes to
Mutect2that caused loss of insertion events immediately following a deletion, as well as general bug fixes to
CombineGVCFs, among others.
These changes, and more, are explained in the full GATK release notes.