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Is there a panel-of-cancer option for somatic variant calling

zyxuezyxue TorontoMember

I am trying to identify somatic variants from 18 pairs of matched tumour/normal samples from a single cancer type.

I've done the tutorial at https://gatkforums.broadinstitute.org/gatk/discussion/11136/how-to-call-somatic-mutations-using-gatk4-mutect2. The idea of panel-of-normals makes a lot of sense to me. So I am wondering if there is an option to call somatic variants of all tumour samples concurrently (hence panel of cancer) w.s.t. the panel of normals, leveraging information from all tumour samples together somehow with GATK4 mutect2?

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  • zyxuezyxue TorontoMember

    Thank you for the clear explanation! Yeah, I meant multi sample form the same tumor. For example all LUAD DNA-Seq samples from the TCGA as the panel of tumor, and all their match normal samples as the panel of normal.

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