v3.2.0#278
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williamrowell merged 4 commits intomainfrom Jan 15, 2026
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* bump: Update TRGT to v5.0.0 - move trgt from upstream of phasing to downstream - updated docs and DAGs - updated image manifest * feat: Replace check_trgt_coverage.py with find_trgt_dropouts.py - new script runs in ~2m for 1M sites, and uses trgt.spanning.sorted.bam, expected ploidy bed, and trgt_catalog as input - removed coverage_dropouts task and run within trgt task
- DeepVaraint is the subworkflow in upstream.wdl with the longest walltime. - DeepVariant subworkflow can accept an array of aBAMs. - Merging aBAMs typically takes ~30 minutes, so passing the array to DeepVariant shaves ~30 minutes off of upstream.wdl walltime.
…pout columns in TRGT documentation
juniper-lake
approved these changes
Jan 15, 2026
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find_trgt_dropouts.pymore accurately detects coverage dropouts at TRGT repeat catalog loci in a small fraction of the time. The output columns for*.trgt.dropouts.txtare now: