4.3.1-1 Release Notes

Highlights:

New tool, deepsomatic for somatic variant calling.
The latest Parabricks toolkit (v4.3.1) is now fully supported on Grace Hopper, see Grace Hopper Superchip.
deepvariant version 1.6.1 updated, new option added.
haplotypecaller bug fixes and 3 new options added.
mutectcaller a few bug fixes.
rna_fq2bam bug fixes and feature added in wrapper.
minimap2 bug fixes, version update, and improved support for ONT data.
fq2bamfast and fq2bam: Bug fixes and performance improvements. Additional option to monitor approximate CPU utilization and host memory usage during execution (--monitor-usage).

New Tools

With Parabricks 4.3.1 we are releasing an accelerated deepsomatic tool. DeepSomatic builds on the deep learning-based variant caller DeepVariant. It processes aligned reads from tumor and normal samples (in BAM or CRAM format), generates pileup image tensors, classifies these tensors using a convolutional neural network, and outputs somatic variants in standard VCF or gVCF files.

Improvements

Tool Updates

haplotypecaller:

Adds the following new options:
- --minimum-mapping-quality
- --mapping-quality-threshold-for-genotyping
- --enable-dynamic-read-disqualification-for-genotyping
Improved performance by leveraging AVX512 instructions for CPU-based PairHMM computation.

mutectcaller:

Improved performance by leveraging AVX512 instructions for CPU-based PairHMM computation.

deepvariant:

Updates to match the baseline version v1.6.1.
Adds the new option --haploid-contigs
Improved performance for short-read mode through increased GPU utilization and kernel optimizations.

rna_fq2bam:

Supports passing --out-chim-type multiple times.

fq2bamfast

Improved alignment performance on Hopper GPUs through increased use of DPX instructions.
Improved performance on multi-GPU runs; for example, on DGX H100.
Improved error detection for improper FASTQ inputs through --in-fq or --in-se-fq. Previously recorded a utf-8 decode error.
Additional option to monitor approximate CPU utilization and host memory usage during execution (--monitor-usage).

fq2bam:

Improved error detection for improper FASTQ inputs through --in-fq or --in-se-fq. Previously recorded a utf-8 decode error.
Additional option to monitor approximate CPU utilization and host memory usage during execution (--monitor-usage).

minimap2:

Updated map-pbmm2 preset to match the updated versions of minimap2 (v2.26) and pbmm2 (v1.13.0).

Bug Fixes

mutectcaller and haplotypecaller: Fixed a wrong alignment offset value in smith-waterman algorithm.
mutectcaller and haplotypecaller: Fixed a crash on GPU when running in low memory mode.
mutectcaller: Fixed the wrong active probability value when the pileup size is 0.
mutectcaller: Fixed a max coverage overflow bug.
rna_fq2bam: Fixed an error when passing "WithinBAM_SoftClip" or "WithinBAM_HardClip" to --out-chim-type.
minimap2: Fixed support for Oxford Nanopore Technologies (ONT) data with minimap2.
fq2bamfast : Fix rare erroneous assertion (Workspace not big enough, expected desiredSize <= cubWorkspaceSize, exiting). Case will now be handled correctly and fall back to CPU recovery if needed.
deepvariant: Fixed bug related to Smith-Waterman computation on CPU.

For further information see the Parabricks datasheet.

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