GATK pipeline from which repository (gatk-workflows or broadinstitute/gatk) should I use?

Follow

WangZiwei

• July 20, 2020 07:28

There are 2 wdl pipeline for mutation calling respectively in:

https://github.com/broadinstitute/gatk/tree/master/scripts/

https://github.com/gatk-workflows/gatk4-somatic-snvs-indels

They look different.

 

Which one is the 'Best Practice' and which one should I refer to?

0

• 

  Samantha (she/her)

  • July 20, 2020 18:02

  Hi WangZiwei,

   

  Thanks for reaching out. You should refer to the WDL pipeline found in the broadinstitute/gatk repository (https://github.com/broadinstitute/gatk/tree/master/scripts/). 

  Please let me know if you have any other questions.

   

  Best,

  Samantha

   

  P.S. The gatk-workflows/gatk4-somatic-snvs-indels repository has been archived (as indicated in the description). Users can still access the workflows by going to the gatk repository.

  1

  Comment actions Permalink
• 

  WangZiwei

  • July 21, 2020 01:59

  Hi Samantha Velasquez ,

  Thank you very much for your timely help.

  My learning path is as follows:

  I googled 'gatk' →

  clicked on the first link（https://gatk.broadinstitute.org/hc/en-us） →

  reached gatk home page →

  clicked on 'getting started' bottom →

  clicked on 'Best Practices Workflow - Getting started with GATK4'(https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4 ) →

  Read Conent 8 'Learn the Best Practices' and clicked on the link →

  reached 'Pipeline Index' which is under construction →

  and I saw several articles on the right side →

  clicked on article 'Somatic short variant discovery (SNVs + Indels)' ( https://gatk.broadinstitute.org/hc/en-us/articles/360035894731-Somatic-short-variant-discovery-SNVs-Indels- ) →

  found 'Reference Implementations' and clicked on github 'b37' link (https://github.com/gatk-workflows/gatk4-somatic-snvs-indels ) which directed me to the archived pipeline

  Maybe some clarifications should be made on the 'Getting started with GATK4' documentations?
  

  My apologize in advance for another question. Some wdl scripts don't seem to have been provided with  their corresponding template json files at https://github.com/broadinstitute/gatk/tree/master/scripts/.  For example gatk/scripts/mutect2_wdl/mutect2.wdl. Where can I found them?

   

  0

  Comment actions Permalink
• 

  Samantha (she/her)

  • July 21, 2020 19:23

  Hi WangZiwei,

   

  Thanks for bringing this up. I have brought this to our User Education team to update the "Somatic short variant discovery (SNVs + Indels)" article and have the GitHub links point to the correct repository instead of the archived one.

  To answer your second question, the json file for gatk/scripts/mutect2_wdl/mutect2.wdl can be found here: https://github.com/broadinstitute/gatk/blob/master/scripts/m2_cromwell_tests/mutect2.inputs.json

  Please let me know if you have any other questions.

   

  Best,

  Samantha

  1

  Comment actions Permalink
• 

  WangZiwei

  • July 22, 2020 04:54

  Hi Samantha Velasquez,

  I'm not sure if other articles in https://gatk.broadinstitute.org/hc/en-us/sections/360007226651-Best-Practices-Workflows also need an update on their GitHub links, since at least most of the links point to the archived repositories.

  Thank you for your generous help.

  0

  Comment actions Permalink
• 

  Samantha (she/her)

  • July 22, 2020 14:27

  Hi WangZiwei,

   

  No problem, I'm happy to help! I'll take a look at the other articles and have them updated if necessary.

  If we can assist you with anything else, please let us know.

   

  Best,

  Samantha

  1

  Comment actions Permalink

Please sign in to leave a comment.