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Redundancy update #425

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wants to merge 26 commits into from
Closed

Redundancy update #425

wants to merge 26 commits into from

Commits on Jun 10, 2021

  1. Basic setup

    @RCollins13
    RCollins13 committed Jun 10, 2021
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  2. Basic changes to reorganize flexible external benchmarking

    @RCollins13
    RCollins13 committed Jun 10, 2021
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  3. Rework inputs in QC WDL to make trio analyses and external benchmarki… 

    …ng optional
    @RCollins13
    RCollins13 committed Jun 10, 2021
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Commits on Jun 18, 2021

  1. Update

    @RCollins13
    RCollins13 committed Jun 18, 2021
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Commits on Jun 22, 2021

  1. Updates to QC for more efficient VID collection per sample

    @RCollins13
    RCollins13 committed Jun 22, 2021
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Commits on Jul 1, 2021

  1. Allow VCF-wide QC plotting to accept VCFs with only allosomes

    @RCollins13
    RCollins13 committed Jul 1, 2021
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Commits on Jul 8, 2021

  1. Subset external benchmarking to contigs of interest

    @RCollins13
    RCollins13 committed Jul 8, 2021
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Commits on Aug 2, 2021

  1. QC updates with XZ IRS

    @RCollins13
    RCollins13 committed Aug 2, 2021
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Commits on Sep 18, 2021

  1. Fix typo in site-level benchmarking plotting code

    @RCollins13
    RCollins13 committed Sep 18, 2021
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  2. Fix external benchmarking helper

    @RCollins13
    RCollins13 committed Sep 18, 2021
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Commits on Sep 19, 2021

  1. Docker update

    @RCollins13
    RCollins13 committed Sep 19, 2021
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  2. Update

    @RCollins13
    RCollins13 committed Sep 19, 2021
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Commits on Sep 20, 2021

  1. Fix per-sample benchmarking in QC

    @RCollins13
    RCollins13 committed Sep 20, 2021
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  2. Updates to per-sample plotting code

    @RCollins13
    RCollins13 committed Sep 20, 2021
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Commits on Sep 21, 2021

  1. Fix compression edge-case for per-sample callset comparison

    @RCollins13
    RCollins13 committed Sep 21, 2021
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Commits on Sep 22, 2021

  1. Add contingengy for edge case where comparison set has no variants

    @RCollins13
    RCollins13 committed Sep 22, 2021
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  2. Make per-sample benchmark plotting more tractable

    @RCollins13
    RCollins13 committed Sep 22, 2021
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Commits on Sep 27, 2021

  1. Make SV type-matching more generous in compare_callsets.sh

    @RCollins13
    RCollins13 committed Sep 27, 2021
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  2. Add contingency for when variant is SVTYPE=CNV

    @RCollins13
    RCollins13 committed Sep 27, 2021
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Commits on Oct 20, 2021

  1. Add contingency for QC on VCFs prior to cleanVCF step 5

    @RCollins13
    RCollins13 committed Oct 20, 2021
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Commits on Oct 25, 2021

  1. Update logic for selecting best matches in AF benchmarking

    @RCollins13
    RCollins13 committed Oct 25, 2021
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  2. Split site-level benchmarking per chromosome

    @RCollins13
    RCollins13 committed Oct 25, 2021
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Commits on Oct 28, 2021

  1. Update QC code before Vahid's PR

    @RCollins13
    RCollins13 committed Oct 28, 2021
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  2. Merge pull request #1 from talkowski-lab/rlc_qc_basics 

    Merge gnomAD v3 QC workflow updates
    @RCollins13
    RCollins13 authored Oct 28, 2021
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Commits on Sep 28, 2022

  1. added scripts to remove redundancies

    @xuefzhao
    xuefzhao committed Sep 28, 2022
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Commits on Oct 7, 2022

  1. recluster script updated

    @xuefzhao
    xuefzhao committed Oct 7, 2022
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