4.2.0-1 Release Notes

Several packages have been updated to GATK 4.3. Support for read lengths of up to 500 base pairs has been added to haplotypecaller and mutectcaller.

Several performance improvements.

A number of bugs have been fixed.

Added markdup, a tool to locate and tag duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.

deepvariant:

  • Major performance improvements.

collectmultiplemetrics:

  • Supports read lengths of up to 500 base pairs.

haplotypecaller:

  • Updated to GATK 4.3.

  • Supports read lengths of up to 500 base pairs.

  • Adds support for the --htvc-bam-output option.

  • --batch is deprecated.

mutectcaller:

  • Updated to GATK 4.3.

  • Supports read lengths of up to 500 base pairs.

  • Adds support for the --run-partition option.

bammetrics

  • Updated to GATK 4.3.

bqsr

  • Clarified error messages.

Improvements spanning multiple tools

  • Added more error checking when writing BAM files using --gpuwrite.

  • Improved performance for BWA alignment, particularly for reads > 250 bases in length.

  • Added GPUDirect Storage (GDS) support for fq2bam (FQ2BAM + BWA-MEM) and associated pipelines.

  • Added a low memory mode for --gpuwrite (affects sorting).

  • deepvariant Could only handle 32 alt alleles per candidate; can now handle up to 64.

  • bamsort Bamsort could fail for certain coordinate sorts.

For further information see the Parabricks datasheet.

© Copyright 2023, Nvidia. Last updated on Dec 13, 2023.