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4.3.2-1 Release Notes

Highlights:

New pipeline, ont_germline for long read ONT variant calling.
minimap2 bug fixes and new features.
Further optimizations and improvements for the Grace Hopper architecture.
Introduced GPU acceleration for CRAM file write operations.

New Tools

With Parabricks 4.3.2 we are releasing an accelerated ont_germline pipeline. The ONT Germline pipeline generates BAM and variants on long read ONT sequences using minimap2 for alignment as well as the DeepVariant variant caller.

Improvements

Tool Updates

minimap2:

Added new options --pbmm2 and --pbmm2-unmapped that include additional processing to match the output of PacBio's pbmm2.
Added ability to use unaligned BAM as input instead of FASTQ (--in-bam).
A new higher compression ratio option for BAM/CRAM files with --gpuwrite.
The nvCOMP DEFLATE compression algorithm options have changed for the parameter --gpuwrite-deflate-algo. Please see --help or the documentation on fq2bam for more details.
Added GPU acceleration for CRAM write operations (--gpuwrite).

fq2bam:

fq2bam has been surpassed by fq2bamfast: the new version of fq2bam with more optimizations for performance. Note that fq2bamfast is no longer present as the fq2bam and fq2bamfast tools have been merged.
Added a new option to use a single-ended unaligned BAM as input instead of a FASTQ file (--in-se-bam).
A new higher compression ratio option for BAM/CRAM files with --gpuwrite.
The nvCOMP DEFLATE compression algorithm options have changed for the parameter --gpuwrite-deflate-algo. Please see --help or the documentation on fq2bam for more details.
Added GPU acceleration for CRAM write operations (--gpuwrite).
Default --min-read-length is 1 base pair; whereas, in fq2bamfast it was 10.
Improved error messaging if paired reads have different names.

deepvariant:

Added a new option --filter-reads-too-long to filter out reads with length > 512bp.
Improved performance and reduced memory consumption when processing long reads (PacBio and ONT data)

haplotypecaller added support for:

Force-calling mode (--htvc-alleles).
The --min-base-quality-score argument.
The --adaptive-pruning argument.
A new annotation AssemblyComplexity can be specified by passing --haplotypecaller-options '-A AssemblyComplexity'.

somatic:

Added more sanity checks to handle possible errors in advance.

germline pipeline and deepvariant_germline:

Grace Hopper (GH200)-specific optimizations.

fq2bam_meth:

Default --min-read-length is now 1 base pair to be in line with fq2bam.
Improved error messaging if paired reads have different names.

Bug Fixes

minimap2:

Fixed a memory leak that was exposed by using a different matching score in the updated preset values.
Fixed a bug that caused some incorrect SA tag values.
Fixed a crash caused by pthread_setaffinity_np.

fq2bam (BWA-MEM + GATK):

Fixed a crash when passing --bwa-options="-C" with no comments in the input fastq file(s).

mutectcaller:

Fixed an invalid GPU memory access in force calling mode (--mutect-alleles).
Fixed additional records in output VCF file when passing --pon.

somatic (Somatic Variant Caller):

Fixed a read group ID conflict error in tumor-normal mode when --tumor-read-group-id-prefix was not passed from the user.

haplotypecaller:

Fixed an out-of-order issue in the output BAM when passing --htvc-bam-output.

deepvariant:

Fixed a bug where certain kernels from multiple pipelines (streams) were launched on the default stream.

For further information see the Parabricks datasheet.

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