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4.3.0-1 Release Notes

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 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 see the Parabricks datasheet.

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