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About ParabricksRelease Notes

4.8.0-1 Release Notes

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Highlights:

  • Updated base container to CUDA 13.3.1 with Rubin support.
  • Updated version of giraffe to v1.75.1.
  • Performance improvements for single-end alignment with giraffe.
  • Added support for supplementary alignment and CRAM file input/output for giraffe.
  • Updated the compatible BWA-MEM version to 0.7.17 for fq2bam and fq2bam_meth.
  • Added Hi-C data support to fq2bam.
  • Better scaling with optimized --run-partition for fq2bam and fq2bam_meth.
  • Performance improvements for fq2bam and fq2bam_meth, with the largest gains for paired-end workflows and minor improvements for single-end workflows.
  • Better host memory management in Marking Duplicates & BQSR step.
  • Performance improvements for long-read technologies with deepvariant.
  • Performance improvements for short-read RNA alignment with minimap2.

Improvements

All tools:

  • Added the --dry-run flag to all Parabricks tools. This flag enables testing a potential command without requiring GPU access.
  • Added the --help-json flag to all Parabricks tools. This prints out the help message in JSON format for easier machine consumption.

Tool Updates

fq2bam, fq2bam_meth, and associated pipelines:

  • The compatible BWA-MEM version has been updated from 0.7.15 to 0.7.17.
  • Added support for additional BWA-MEM commandline arguments: -S, -P, -5, and -q via the --bwa-options commandline parameter.
  • Hi-C data is now supported in fq2bam using the aforementioned arguments, which can be provided as --bwa-options="-SP5M <additional args>".
  • Improved end-to-end BAM generation performance, mainly for paired-end alignment, with smaller improvements for single-end alignment.
  • Better scaling with optimized --run-partition when using more GPUs.

fq2bam:

  • Updated the default CPU threading configuration for improved end-to-end runtime. The option --bwa-primary-cpus now defaults to auto, which selects 16 primary CPU threads per GPU, and --bwa-cpu-thread-pool now defaults to 1. Both options can still be set manually to override the defaults.

deepvariant:

  • Performance improvements for long-read technologies (PacBio and ONT).

deepvariant, deepsomatic, and pangenome_aware_deepvariant:

  • Updated TensorRT from version 10.14.1.48 to 11.3.0.99.
  • Added timing summary for each stage when enabling --verbose.
  • Added validation of multiallelic call outputs before predictions are merged. Parabricks now exits with a locus-specific error if the expected alternate allele combinations are missing or invalid, or if records disagree on the canonical variant.

haplotypecaller, mutectcaller:

  • Introduced auto mode for --num-streams-per-gpu that automatically selects the number of streams per GPU based on available GPU memory. This value can be overridden by providing an explicit value.

giraffe:

  • Updated the baseline vg version from 1.70.0 to 1.75.1. New index files must be generated with vg v1.75.1; refer to the index generation section.
  • Only GBZ version 1 graphs are supported. Starting with vg 1.72.0, vg autoindex and vg gbwt write GBZ version 2 by default, which stores node sequences zstd-compressed. Loading such a graph now fails with an error naming the conversion command; refer to Supported GBZ version.
  • Added CRAM output, selected by passing --out-bam a path ending in .cram. This requires --ref, and --run-ref-verification is recommended to check the reference against the graph.
  • Added support for aligning single-end CRAM input with --in-se-cram, together with --in-cram-ref for aligned input and --cram-read-threads to control decode threads.
  • Added --ultima-tags to carry the Ultima per-base tp and t0 auxiliary tags from CRAM input through to the output, and --tp-output-order to select whether those values follow the output SEQ or the sequencing direction.
  • Performance improvements for single-end alignment.

giraffe and pangenome_germline:

  • Added --supplementary to identify and report supplementary alignments, for both single-end and paired-end reads. It is disabled by default.

minimap2:

  • Added proper fragment handling of pair-ended FASTQ inputs.
  • Moved the seeding stage to GPU to reduce CPU load. The --seeding-chaining-on-gpu [on|off|auto] flag controls where both the seeding and chaining stage are computed.
  • Introduced an “auto” mode for the best performance, which tunes parameters based on the device memory and preset. The parameters can be overridden by providing an explicit value.
  • Added a read group tag to each output read.

bqsr, fq2bam, fq2bam_meth, giraffe, minimap2, deepvariant_germline, germline, ont_germline, pacbio_germline, somatic:

  • Updated the help message of --knowSites when enabling Base Quality Score Recalibration (BQSR).

bamsort, fq2bam, fq2bam_meth, giraffe, minimap2, deepvariant_germline, germline, ont_germline, pacbio_germline, somatic:

  • Skipped checking LB (library preparation identifier) when marking duplicates is disabled.

fq2bam, fq2bam_meth, giraffe, minimap2, rna_fq2bam, bamsort, and associated pipelines:

  • Optimized host memory usage during BAM and CRAM file writing.

applybqsr:

  • Clarified that CRAM input and output files are accepted for the options named --in-bam and --out-bam, respectively.

Bug Fixes

All tools that take a reference FASTA:

  • Fixed handling of Windows (CRLF) line endings in the reference FASTA. A trailing carriage return no longer leaks into contig names or sequence data.

deepvariant, deepsomatic, and pangenome_aware_deepvariant:

  • Fixed bug affecting how read support is computed for duplicate reads.

deepvariant:

  • The --disable-small-model argument is no longer required with WES mode. Parabricks now matches Google DeepVariant’s default behavior by disabling the small model in WES mode.
  • Fixed bug causing improper operation of the --keep-duplicates flag.
  • Fixed a rare edge-case bug that occasionally caused a deadlock when processing PacBio or ONT data.

deepsomatic:

  • Fixed bug causing incorrect handling of the --no-channel-insert-size flag.

haplotypecaller:

  • Fixed an edge-case bug that occurred during gVCF writing.

germline:

  • Added additional argument checks to prevent runs from failing in haplotypecaller.

deepvariant_germline, germline, ont_germline, pacbio_germline, pangenome_germline, and somatic:

  • The option --preserve-file-symlinks now properly works for pipeline commands.

fq2bam, fq2bam_meth, giraffe, minimap2, rna_fq2bam, bamsort, and associated pipelines:

  • Fixed a bug that could cause runs using --gpuwrite to fail with an error during BAM writing. An internal check was overly strict, so valid runs could have been flagged as errors.

For further information refer to the Parabricks datasheet.