About ParabricksRelease Notes

4.5.0-1 Release Notes

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Highlights:

  • Support for the following NVIDIA Blackwell GPU architectures: SM_100 and SM_120.
  • As of v4.5 we are dropping support for the Volta (V100) line of GPUs.
  • Splice-aware support and performance improvements for minimap2.
  • Performance improvements for giraffe.
  • Marking duplicates is now on by default for giraffe. Use --no-markdups to turn off marking duplicates.
  • Faster rna_fq2bam with --num-streams-per-gpu.
  • Performance improvements for force-calling mode in haplotypecaller and mutectcaller.

Improvements

Tool Updates

fq2bam and fq2bam_meth:

  • Added --in-fq-list and --in-se-fq-list support. You can specify a file containing a list of paired-end or single-end FASTQ file paths along with their corresponding read group information.
  • Recovery mode has been improved to avoid falling back to CPU—enhancing performance. This may happen often when an input FASTQ produces a large amount of SMEMs (SuperMaximal Exact Matches) per read.
  • Peak host memory use can be indirectly modified by changing --bwa-normalized-queue-capacity.
  • Improved performance on devices with compute capability SM_90 (e.g. H100, H200) and SM_100 (e.g. B200).

giraffe:

  • Improved performance across the board.
  • Marking duplicates is now enabled by default. The option --no-markdups has been added to skip the marking duplicates step.
  • Added support for --ref-paths. This option allows to specify an ordered list of paths in the graph and helps supporting pangenome graphs containing multiple reference paths in variant calling pipelines.
  • Added --in-fq-list and --in-se-fq-list support. You can specify a file containing a list of paired-end or single-end FASTQ file paths along with their corresponding read group information.
  • Added --copy-comment which allows the user to copy FASTQ comments to BAM output via the auxiliary tag. Similar to -C in fq2bam and BWA-MEM.

markdup:

  • Added --markdups-single-ended-start-end to mark duplicate on single-ended reads by 5’ and 3’ end.

minimap2:

  • Added support for --preset options splice and splice:hq.
  • Performance improvements.
  • Added --max-queue-reads and --nstreams performance options.

rna_fq2bam:

  • Added --num-streams-per-gpu to support multiple GPU streams.

mutectcaller:

  • Faster force-variant call --mutect-alleles in mutectcaller.

haplotypecaller:

  • Faster force-variant call --htvc-alleles in haplotypecaller.

deepvariant:

  • Added support for --keep_legacy_allele_counter_behavior.

deepvariant:

  • Added --use-tf32 to utilize tensor cores during inference to achieve better performance on Ampere+ GPUs. Note the accuracy might be slightly impacted because of tf32 lower precision.

General

  • Support for the following NVIDIA Blackwell GPU architectures: SM_100 and SM_120.
  • Improved error messaging when Parabricks receives signals from the OS, such as out-of-memory (OOM) killer events.

Bug Fixes

fq2bam_meth:

  • Fixed crash which occurred when the input FASTQ did not contain read comments.

haplotypecaller:

  • Fixed a hash table overflow in De Bruijn graph.

markdup:

  • Fixed a crash which occurred when the input BAM did not have a read group line. Error will be handled at the start.
  • Fixed correctness issue when the read queryname had non-numeric characters in the colon-delimited end of the name.

For further information refer to the Parabricks datasheet.