Create Panel of Normals Issue

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Yuwei Bao

• October 12, 2022 00:51

Hi everyone:

I am using GATK v4.2.6.1 and I have trouble producing Panel of Normal for somatic mutation calling using the following workflow from the tutorial :

 

Step 1: Run Mutect2 in tumor-only mode for each normal sample: (this step succeed, I obtained multiple normal_pon.vcf.gz)
Step 2: Create a GenomicsDB from the normal Mutect2 calls:

gatk GenomicsDBImport -R reference.fasta -L 2L \
        --genomicsdb-workspace-path pon_db \
        -V normal1.vcf.gz \
        -V normal2.vcf.gz \
        -V normal3.vcf.gz

Then I obtained a folder named pon_db included one folder named 2L$1$23513712 and some .json files.

Step 3: Combine the normal calls using CreateSomaticPanelOfNormals:

    gatk CreateSomaticPanelOfNormals -R reference.fasta \
      --germline-resource known_variants.vcf.gz \
      -V pon_db \
      -O pon.vcf.gz

But I got the error :

work_path/pon_db/. Error was: It isn't a regular file. What files are expected in pon_db folder? And what should I do to fix this issue?

 

Thank you very much!

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• 

  Anthony DiCi

  • October 13, 2022 14:55

  Hi Yuwei Bao,

  Thank you for writing to the GATK forum! I hope that we can help you sort this out.

  Before I bring this to our developers for their insight, could you please provide your entire command line and program log? Please include all exceptions, warnings, and or error messages. We will then be better able to diagnose the problem you are experiencing.

  I hope to hear back from you soon!

  Best,
  Anthony

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  Anthony DiCi

  • October 24, 2022 13:41

  Hi Yuwei Bao,

  We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!

  Kind regards,

  Anthony​

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