4.2.1-1 Release Notes

NVIDIA Parabricks v4.3.1

Two new beta tools have been released: fq2bamfast and minimap2.

A new beta pipeline has been released: pacbio_germline.

Performance improvements include fq2bamfast, a faster version of the existing fq2bam and the ability to run the variant caller in germline and deepvariant_germline in parallel with BAM generation.

A number of bugs have been fixed. Most notably, fq2bam read filtering could have failed with read sizes more than ~500 basepairs.

With this release we have added two new tools:

We have also added one new pipeline:

The new beta fq2bamfast is a re-implementation of accelerated BWA-MEM present in fq2bam to better utilize GPUs such as A100 and H100.

Tool Updates


  • Adds the following new options:

    • --active-probability-threshold

    • --genotype-germline-sites

    • --genotype-pon-sites

    • --initial-tumor-lod

    • --mutect-bam-output

    • --pruning-lod-threshold

    • --tumor-lod-to-emit

    • -max-reads-per-alignment-start (as part of the --mutectcaller-options option)

fq2bam and associated pipelines: germline pipeline, deepvariant_pipeline, and somatic pipeline:

  • New compression options for --gpuwrite: use --gpuwrite-deflate-algo 3 for more compression at slightly slower speed and --gpuwrite-deflate-algo 0 for more speed, which continues to be the default.

  • Fix edge case with FASTQ filtering.

Improvements spanning multiple tools

For further information see the Parabricks datasheet.

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