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base repository: gatk-workflows/gatk4-somatic-snvs-indels
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base: 2.2.0
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head repository: gatk-workflows/gatk4-somatic-snvs-indels
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compare: master
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  • 15 commits
  • 9 files changed
  • 2 contributors

Commits on Oct 18, 2018

  1. added numbered bullet points to README.md (#12)

    Zhuyi Xue authored and bshifaw committed Oct 18, 2018
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Commits on Nov 7, 2018

  1. Wdlupdate (#13) 

    * updated pon file bucket location

* minor edits to ReadMe
    bshifaw authored Nov 7, 2018
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  2. README.md (#14)

    bshifaw authored Nov 7, 2018
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Commits on Feb 1, 2019

  1. Dev (#15) 

    * README.md

* Update to gatk4.1 (https://github.com/broadinstitute/gatk/tree/4.1.0.0/scripts/mutect2_wdl)

* Updated forum links in Readme

* changed ref file VM path to google bucket path
    bshifaw authored Feb 1, 2019
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  2. Dev (#16) 

    * README.md

* Update to gatk4.1

* Updated forum links in Readme

* changed ref file VM path to google bucket path

* updated import link to git tag url
    bshifaw authored Feb 1, 2019
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Commits on Apr 5, 2019

  1. Dev (#17) 

    * updated to GATK4.1.1.0

* minor edits

* changed import to dev for pon

* updated filter bias variable

* updated output variable names, removed artifact_mode from normal-normal

* changed index to idx

* removed artifact_modes

* updated import to next release: 2.4.0
    bshifaw authored Apr 5, 2019
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  2. Dev (#18) 

    * specified gatk version in readme
    bshifaw authored Apr 5, 2019
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Commits on Apr 25, 2019

  1. Dev (#19) 

    * Added Funcotator note to readme

* Update to gatk4.1.2.0

* updated input variable for mutect2
    bshifaw authored Apr 25, 2019
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  2. Dev (#20) 

    * correction to output variable
    bshifaw authored Apr 25, 2019
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  3. Dev (#21) 

    * README.md

* Update to gatk4.1

* Updated forum links in Readme

* changed ref file VM path to google bucket path

* updated import link to git tag url

* updated to GATK4.1.1.0

* minor edits

* changed import to dev for pon

* updated filter bias variable

* updated filter bias variable

* updated output variable names, removed artifact_mode from normal-normal

* changed index to idx

* removed artifact_modes

* updated import to next release: 2.4.0

* specified gatk version in readme

* Added Funcotator note to readme

* Update to gatk4.1.2.0

* updated input variable for mutect2

* correctin to input vairalbe

* correction to output variable
    bshifaw authored Apr 25, 2019
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  4. update output variable (#22)

    bshifaw authored Apr 25, 2019
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Commits on Aug 19, 2019

  1. Dev (#24) 

    * README.md

* Update to gatk4.1

* Updated forum links in Readme

* changed ref file VM path to google bucket path

* updated import link to git tag url

* updated to GATK4.1.1.0

* minor edits

* changed import to dev for pon

* updated filter bias variable

* updated filter bias variable

* updated output variable names, removed artifact_mode from normal-normal

* changed index to idx

* removed artifact_modes

* updated import to next release: 2.4.0

* specified gatk version in readme

* Added Funcotator note to readme

* Update to gatk4.1.2.0

* updated input variable for mutect2

* correctin to input vairalbe

* correction to output variable

* corrected variable name and simplified json
    bshifaw authored Aug 19, 2019
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Commits on Oct 15, 2019

  1. GATK 4.1.4.0 Dev (#27) 

    * README.md

* Update to gatk4.1

* Updated forum links in Readme

* changed ref file VM path to google bucket path

* updated import link to git tag url

* updated to GATK4.1.1.0

* minor edits

* changed import to dev for pon

* updated filter bias variable

* updated filter bias variable

* updated output variable names, removed artifact_mode from normal-normal

* changed index to idx

* removed artifact_modes

* updated import to next release: 2.4.0

* specified gatk version in readme

* Added Funcotator note to readme

* Update to gatk4.1.2.0

* updated input variable for mutect2

* correctin to input vairalbe

* correction to output variable

* corrected variable name and simplified json

* renamed input json, removed optional variables from json, updated regular mutect2 wdl with wdl version 1, updated mutect_pon wdl with wdl version 1

* removed nio wdl

* minor update

* removed comments in json because later version of cromwell throws error, replaced oncotator in json variables with funcotator

* corrections to import url for pon wdl

* mutect2 WDL and pon WDL had inconsistent input names

* mutect2 WDL and pon WDL had inconsistent input names

* added standard_runtime to pon

* add runtime structs

* add runtime structs for mergevcf

* Update mutect2_pon.wdl

minor spacing edit

* cleaned up input variables

* Update README.md

Replaced firecloud link with terra

* updated docker to 4.1.4.0, updated import url to latest release
    bshifaw authored Oct 15, 2019
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Commits on Jan 13, 2020

  1. Dev (#30) 

    * updated docker to 4.1.4.1, updated mutect.wdl to 4.1.4.1 gatk release
    bshifaw authored Jan 13, 2020
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Commits on Mar 9, 2020

  1. Dev (#34) 

    * Update GATK links and contact us message
* minor update
    bshifaw authored Mar 9, 2020
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