About ParabricksRelease Notes

4.3.0-1 Release Notes

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Highlights:

  • New tool, fq2bam_meth for accelerated DNA methylation analysis.
  • Germline resource mode and force calling mode are supported in mutectcaller.
  • Support for writing CRAM files using queryname-based sorting has been added into bamsort.
  • Parabricks toolkit (v4.2) is now fully supported on Grace Hopper, refer to NVIDIA Grace CPU Platforms.
  • Performance improvements in germline and deepvariant_germline running on DGX H100.
  • deepvariant version 1.6 updated.
  • minimap2 performance improvements and bug fixes.
  • fq2bamfast performance improvements and bug fixes.

New Tools

New tool for bisulfite sequencing data fq2bam_meth based on bwa-meth. Our tool, fq2bam_meth, implements compatible pre- and post-processing around BWA MEM for DNA methylation analysis. It uses the same accelerated alignment code as is used in fq2bamfast to produce fast and accurate alignment.

Improvements

Tool Updates

bamsort:

  • Supports CRAM file write on queryname-based sorting. It auto-detects cram file extension on output file.

mutectcaller:

  • Adds the following new options:

    • --mutect-germline-resource
    • --mutect-alleles
    • --force-call-filtered-alleles

deepvariant:

  • Updates to match the baseline version v1.6.

minimap2:

  • Reduced reader buffer size to shorten the time it takes to start processing.

fq2bamfast

  • Speed improvements.
  • Added support for BWA MEM options: -B (values up to 15), -T, -L, and -U.
  • Added support for reads longer than 500 bp using CPU recovery mode (note that speed will be slower and memory usage will be higher). Set --max-read-length to the desired max read length for the FASTQ filter.

Improvements Spanning Multiple Tools

  • Better messaging in filehandle when reading index files to avoid user confusion.
  • Better error checking when reading FASTQ files: checks that each FASTQ read name line starts with ’@’.

Bug Fixes

  • mutectcaller and haplotypecaller: Fixed a random segfault in bamOut mode.
  • haplotypecaller: Fixed an “allele out of index” bug in gvcf mode.
  • haplotypecaller: Fixed an GPU shared memory overflow bug in gvcf mode.
  • haplotypecaller, mutectcaller and deepvariant: Fixed a wrong return value 0 when the run fails.
  • minimap2: Corrected banner name when running minimap2.
  • minimap2: Fixed overflow issue in postsort.
  • minimap2: Removed max read size requirement that made some inputs unable to run.
  • fq2bamfast: Fix for edge case (related to multiple hits) with -C option in BWA MEM to copy auxiliary tags from FASTQ comments.

For further information refer to the Parabricks datasheet.