New Tools

NVIDIA Parabricks v4.2.0

Added markdup, a tool to locate and tag duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.

deepvariant:

  • Major performance improvements.

collectmultiplemetrics:

  • Supports read lengths of up to 500 base pairs.

haplotypecaller:

  • Updated to GATK 4.3.

  • Supports read lengths of up to 500 base pairs.

  • Adds support for the --htvc-bam-output option.

  • --batch is deprecated.

mutectcaller:

  • Updated to GATK 4.3.

  • Supports read lengths of up to 500 base pairs.

  • Adds support for the --run-partition option.

bammetrics

  • Updated to GATK 4.3.

bqsr

  • Clarified error messages.

Improvements spanning multiple tools

  • Added more error checking when writing BAM files using --gpuwrite.

  • Improved performance for BWA alignment, particularly for reads > 250 bases in length.

  • Added GPUDirect Storage (GDS) support for fq2bam (FQ2BAM + BWA-MEM) and associated pipelines.

  • Added a low memory mode for --gpuwrite (affects sorting).

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