Improvements
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Adds the following new options:
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--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)
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fq2bam and associated pipelines: germline pipeline, deepvariant_pipeline, and somatic pipeline:
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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.
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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.