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PON and germline files for Mutect2 Tumor-only mode

Hi!

I am applying Mutect2 in tumor-only.mode having hg19 as reference and samples resulting of targeted sequencing (not only coding gene parts but also some non coding regions), I found this: https://console.cloud.google.com/storage/browser/gatk-best-practices/somatic-b37%2F;tab=objects?prefix=&forceOnObjectsSortingFiltering=false. This bundle is used for b37 which is equivalent to hg19 (not 100% similar).

export PON="/filepath/Mutect2-WGS-panel-b37-hg19.vcf"
 export GERM="/filepath/af-only-gnomad-hg19.raw.sites.vcf" 
 export VCF="/filepath/${patient_id}/${patient_id}.recalibrated.vcf"
 srun /mnt/beegfs/apptainer/images/gatk4.sif gatk Mutect2 \
-R $GENOME \
-I $RECBAM \
--panel-of-normals $PON \
--germline-resource $GERM \
-O $VCF

Can Mutect2-WGS-panel-b37.vcf be used as PON and af-only-gnomad as germline for Mutect2 Tumor Only Mode?

If yes, I going to use picard LiftTools to convert b37 into hg19 using b37tohg19.chain from https://github.com/broadgsa/gatk/blob/master/public/chainFiles/b37tohg19.chain.

Best Regards, Manuel

gatk variant-calling mutect2
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updated by Zhenyu Zhang Zhenyu Zhang • written by Manuel • Manuel

I've edited your post so your title stays descriptive but is also shorter and not a question.

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written by Ram Ram

Are you sure the PoN you found is for tumor-only? I don't see tumor-only in its name, unless some other source told you so.

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written by Zhenyu Zhang Zhenyu Zhang

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