Improvements
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-optionsoption)
fq2bam and associated pipelines: germline pipeline, deepvariant_pipeline, and somatic pipeline:
New compression options for
--gpuwrite: use--gpuwrite-deflate-algo 3for more compression at slightly slower speed and--gpuwrite-deflate-algo 0for more speed, which continues to be the default.Fix edge case with FASTQ filtering.
Added the
--read-from-tmp-diroption to germline pipeline and deepvariant_pipeline. It will run the variant caller in parallel with BAM generation. It has been tested on A100 and H100 but might cause out-of-memory on other GPUs.Added the
--fq2bamfastoption to germline pipeline, deepvariant_pipeline, and somatic pipeline to use fq2bamfast for alignment.