Script for using same GATK tool(s) on multiple sample files

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Youssef Tawfik

• August 01, 2021 16:32

How do I write a script so I can use the same tool (I'm mostly using HaplotypeCaller and GenotypeGVCFs) on multiple sample files (I have 60 sample files) without having to run the same command for each sample file one by one and still have in the end a VCF file for each sample file?

I'm using GATK on Docker and I tried following the steps here: https://support.terra.bio/hc/en-us/articles/360037127992--1-howto-Write-your-first-WDL-script-running-GATK-HaplotypeCaller but I couldn't do it eventually and had error to access the wdltool.jar

I'm still new to command-line and coding so I'm not sure what to do exactly, and I haven't even understood fully the article I put above but I applied the steps exactly as written.

I appreciate your help.

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  Genevieve Brandt (she/her)

  • August 03, 2021 22:39

  Hi Youssef Tawfik,

  Our GATK support team is focused on GATK specific questions and questions regarding GATK abnormal results. Here is our support policy for more information. You can leave this post here in case other users can provide insight and you can also check out these resources for more information:

  • Mailing list for general conversation with the WDL community
  • Github issues for suggestions and discussions on the WDL specification
  • Slack for real time chat with other community members
  • Stack Overflow for asking questions about writing and using WDL
  • (From openwdl.org)
  • WDL docs:
    • WDL Github Spec
    • Docs
    • Getting Started with WDL

  Thanks for posting here on the GATK forum where you can engage with other people new to GATK and the command line!

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