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feat(HiPhase): Phase TRGT VCF with HiPhase #107

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wants to merge 16 commits into from
Closed

feat(HiPhase): Phase TRGT VCF with HiPhase #107

wants to merge 16 commits into from

Commits on Jan 10, 2024

  1. feat(HiPhase): Phase TRGT VCF with HiPhase 

    Updated HiPhase to v1.1, and added TRGT to the HiPhase inputs.  HiPhase will now concurrently phase DeepVariant, PBSV, and TRGT VCFs, and apply the haplotype tags and phase set tags to the aligned BAM.  Because of this change, BAM merging was moved upstream of HiPhase.
    @williamrowell
    williamrowell committed Jan 10, 2024
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Commits on Jan 17, 2024

  1. Updated submodule to increase memory for HiPhase, DeepVariant, and PBSV

    @williamrowell
    williamrowell committed Jan 17, 2024
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Commits on Feb 16, 2024

  1. Merge branch 'develop' into feature/hiphase-1.1

    @williamrowell
    williamrowell authored Feb 16, 2024
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  2. update wdl-ci config file after successful tests

    @github-actions
    github-actions[bot] committed Feb 16, 2024
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  3. Merge branch 'develop' into feature/hiphase-1.1

    @williamrowell
    williamrowell authored Feb 16, 2024
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  4. Fix TRGT version number in docs

    @williamrowell
    williamrowell committed Feb 16, 2024
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Commits on Feb 17, 2024

  1. fix(pbsv): Set mem for pbsv_discover to 10GB.

    @williamrowell
    williamrowell committed Feb 17, 2024
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  2. update wdl-ci config file after successful tests

    @github-actions
    github-actions[bot] committed Feb 17, 2024
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  3. fix(deepvariant): Decompress custom deepvariant models to writable lo… 

    …cations.
    @williamrowell
    williamrowell committed Feb 17, 2024
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  4. Merge remote-tracking branch 'refs/remotes/origin/feature/hiphase-1.1… 

    …' into feature/hiphase-1.1
    @williamrowell
    williamrowell committed Feb 17, 2024
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  5. update wdl-ci config file after successful tests

    @github-actions
    github-actions[bot] committed Feb 17, 2024
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Commits on Mar 9, 2024

  1. Merge branch 'develop' into feature/hiphase-1.1

    @williamrowell
    williamrowell authored Mar 9, 2024
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  2. feat(trgt): Normalize TRGT output names by providing explicit sample.… 

    …ref prefix.
    @williamrowell
    williamrowell committed Mar 9, 2024
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  3. feat(hiphase): Normalize HiPhase BAM outputs if only one BAM is to be… 

    … haplotagged.
    @williamrowell
    williamrowell committed Mar 9, 2024
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  4. Merge remote-tracking branch 'refs/remotes/origin/feature/hiphase-1.1… 

    …' into feature/hiphase-1.1
    @williamrowell
    williamrowell committed Mar 9, 2024
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  5. fix(glnexus): Clean up large intermediate files from glnexus.

    @williamrowell
    williamrowell committed Mar 9, 2024
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