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PoN creation : --germline_resource option

escaonescaon Limoges, FranceMember

Dear all,

I think it's a bit confusing whether or not one should use --germline_resource option for Mutect2 tumor-only runs prior to PoN creation.

First link :

One option that is not used here is to include a germline resource with --germline-resource. Remember from section 1 this resource must contain AF population allele frequencies in the INFO column. Use of this resource in tumor-only mode, just as in somatic mode, allows upfront filtering of common germline variant alleles. This effectively omits common germline variant alleles from the PoN.

If i use google searching for "CreateSomaticPanelOfNormals" : link :

Step 1. Run Mutect2 in tumor-only mode for each normal sample.
gatk-launch --javaOptions "-Xmx4g" Mutect2 \
-R ref_fasta.fa \
-I normal1.bam \
-tumor normal1_sample_name \
--germline_resource af-only-gnomad.vcf.gz \
-L intervals.list \
-O normal1_for_pon.vcf.gz

If I go there looking for latest doc :

Step 1. Run Mutect2 in tumor-only mode for each normal sample.
gatk Mutect2 \
-R reference.fa \
-I normal1.bam \
-tumor normal1_sample_name \
-O normal1_for_pon.vcf.gz

Question : Why does the second link still exists ? I find it pretty missleading, given that from my understanding, we should not use --germline-resource option for PoN creation.



  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    The first link is to the beta documentation. I think google still goes to that version of the docs. But, the second link is to the GATK4 stable latest tool documents. You should use the second link.


    P.S. I will let the team know and see if we can fix the google search.

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