4.3.0-1 Release Notes

NVIDIA Parabricks v4.3.1 Download PDF

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, see Grace Hopper Superchip.

  • 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 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.

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 (Beta):

  • 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 '@'.

For further information see the Parabricks datasheet.

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