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PacificBiosciences / pb-human-wgs-workflow-snakemake

DEPRECATED - Workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads
BSD 3-Clause Clear License
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trgt de novo #172

Closed lauragails closed 9 months ago

lauragails commented 9 months ago

Hello! Is there any plan to put trgt de novo in the pipeline?

I only have 1 trio so it's easy to run as a stand-alone, but was curious for the future.

Thank you, Laura

williamrowell commented 9 months ago

This workflow is no longer under active development. All future development will be under the PacificBiosciences/HiFi-human-WGS-WDL workflow. We haven't yet added TRGTdn, but may in the future.

lauragails commented 9 months ago

Got it, thank you Billy!

lauragails commented 9 months ago

(Is there any benefit to running the new pipeline for runs from ~1Y ago?)

williamrowell commented 9 months ago

It's really up to you. The largest gains are in the additions of newer tools like Paraphase (typing a set of genes in segmental duplications) and HiFiCNV (depth-based CNV detection). We've also replaced WhatsHap with an internally developed tool, HiPhase, that can phase both SVs and small variants (and STRs, to be implemented soon in the WDL workflow). There are a lot of version updates for other tools as well. De novo assembly was removed to a separate workflow that will be public soon, and nothing changed for tertiary analysis.

You can find a full list of outputs here.