Improvements

NVIDIA Parabricks v4.3.1

bamsort:

  • Supports CRAM file write on queryname-based sorting. It auto-detects cram file extension on output file.

mutectcaller:

  • Adds the following new options:

    • --mutect-germline-resource

    • --mutect-alleles

    • --force-call-filtered-alleles

deepvariant:

  • Updates to match the baseline version v1.6.

minimap2 (Beta):

  • Reduced reader buffer size to shorten the time it takes to start processing.

fq2bamfast:

  • Speed improvements.

  • Added support for BWA MEM options: -B (values up to 15), -T, -L, and -U.

  • Added support for reads longer than 500 bp using CPU recovery mode (note that speed will be slower and memory usage will be higher). Set --max-read-length to the desired max read length for the FASTQ filter.

  • Better messaging in filehandle when reading index files to avoid user confusion.

  • Better error checking when reading FASTQ files: checks that each FASTQ read name line starts with '@'.

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