Improvements

mutectcaller:

  • Adds the following new options:

    • --active-probability-threshold

    • --genotype-germline-sites

    • --genotype-pon-sites

    • --initial-tumor-lod

    • --mutect-bam-output

    • --pruning-lod-threshold

    • --tumor-lod-to-emit

    • -max-reads-per-alignment-start (as part of the --mutectcaller-options option)

fq2bam and associated pipelines: germline pipeline, deepvariant_pipeline, and somatic pipeline:

  • New compression options for --gpuwrite: use --gpuwrite-deflate-algo 3 for more compression at slightly slower speed and --gpuwrite-deflate-algo 0 for more speed, which continues to be the default.

  • Fix edge case with FASTQ filtering.

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