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[VS-693] Add support for VQSR Lite to GvsCreateFilterSet #8157

Merged
merged 24 commits into from
Feb 2, 2023
Merged

[VS-693] Add support for VQSR Lite to GvsCreateFilterSet #8157

merged 24 commits into from
Feb 2, 2023

Commits on Oct 17, 2022

  1. Added a new suite of tools for variant filtering based on site-level … 

    …annotations. (#7954)

* Adds wdl that tests joint VCF filtering tools (#7932)

* adding filtering wdl

* renaming pipeline

* addressing comments

* added bash

* renaming json

* adding glob to extract for extra files

* changing dollar signs

* small comments

* Added changes for specifying model backend and other tweaks to WDLs and environment.

* Added classes for representing a collection of labeled variant annotations.

* Added interfaces for modeling and scoring backends.

* Added a new suite of tools for variant filtering based on site-level annotations.

* Added integration tests.

* Added test resources and expected results.

* Miscellaneous changes.

* Removed non-ASCII characters.

* Added documentation for TrainVariantAnnotationsModel and addressed review comments.

Co-authored-by: meganshand <[email protected]>
    @samuelklee @meganshand @rsasch
    2 people authored and rsasch committed Oct 17, 2022
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  2. Added toggle for selecting resource-matching strategies and miscellan… 

    …eous minor fixes to new annotation-based filtering tools. (#8049)
    @samuelklee @rsasch
    samuelklee authored and rsasch committed Oct 17, 2022
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  3. Adding use_allele_specific_annotation arg and fixing task with empty … 

    …input in JointVcfFiltering WDL (#8027)

* Small changes to JointVCFFiltering WDL

* making default for use_allele_specific_annotations

* addressing comments
    @meganshand @rsasch
    meganshand authored and rsasch committed Oct 17, 2022
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  4. first stab

    @rsasch
    rsasch committed Oct 17, 2022
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Commits on Oct 18, 2022

  1. wire through WDL changes

    @rsasch
    rsasch committed Oct 18, 2022
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  2. Merge branch 'ah_var_store' into rsa_vqsr_lite_poc

    @rsasch
    rsasch committed Oct 18, 2022
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  3. fixed typo

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    rsasch committed Oct 18, 2022
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  4. set model_backend input value

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    rsasch committed Oct 18, 2022
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  5. add gatk_override to JointVcfFiltering call

    @rsasch
    rsasch committed Oct 18, 2022
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  6. typo in indel_annotations

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    rsasch committed Oct 18, 2022
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Commits on Oct 19, 2022

  1. make model_backend optional

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    rsasch committed Oct 19, 2022
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  2. tabs and spaces

    @rsasch
    rsasch committed Oct 19, 2022
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  3. make all model_backends optional

    @rsasch
    rsasch committed Oct 19, 2022
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  4. use gatk 4.3.0

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Commits on Oct 20, 2022

  1. no point in changing the table names as this is a POC

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    rsasch committed Oct 20, 2022
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Commits on Oct 24, 2022

  1. Merge branch 'ah_var_store' into rsa_vqsr_lite_poc

    @rsasch
    rsasch committed Oct 24, 2022
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Commits on Jan 4, 2023

  1. adding new branch to dockstore

    @koncheto-broad
    koncheto-broad committed Jan 4, 2023
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Commits on Jan 6, 2023

  1. adding in branching logic for classic VQSR vs VQSR-Lite

    @koncheto-broad
    koncheto-broad committed Jan 6, 2023
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Commits on Jan 9, 2023

  1. implementing the separate schemas for the VQSR vs VQSR-Lite branches,… 

    … including Java changes necessary to produce the different tsv files
    @koncheto-broad
    koncheto-broad committed Jan 9, 2023
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Commits on Jan 10, 2023

  1. passing classic flag to indel run of CreateFilteringFiles

    @koncheto-broad
    koncheto-broad committed Jan 10, 2023
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Commits on Jan 17, 2023

  1. Update GvsCreateFilterSet.wdl 

    cleaning up verbiage
    @koncheto-broad
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Commits on Jan 23, 2023

  1. Removed mapping error rate from estimate of denoised copy ratios outp… 

    …ut by gCNV and updated sklearn. (#7261)
    @samuelklee @koncheto-broad
    samuelklee authored and koncheto-broad committed Jan 23, 2023
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Commits on Jan 24, 2023

  1. Merge branch 'ah_var_store' into VS-693_VQSR_lite

    @koncheto-broad
    koncheto-broad committed Jan 24, 2023
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Commits on Jan 30, 2023

  1. cleanup up sloppy comment

    @koncheto-broad
    koncheto-broad committed Jan 30, 2023
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