About ParabricksRelease Notes

4.2.0-1 Release Notes

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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.

Improvements

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 (BWA-MEM + GATK) and associated pipelines.
  • Added a low memory mode for --gpuwrite (affects sorting).

Bug Fixes

  • 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 refer to the Parabricks datasheet.