Improvements

NVIDIA Parabricks v4.3.1

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).

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