I have to call somatic variant for mutate sample with no matching normal.
I have read the GATK mutect2 page, but still not understand the tumor only mode..
They call that tumor only mode and say "call on each normal sample in this mode", but I don't have normal, so I don't understand what I should do.
Thanks for any explanation:
(ii) Tumor-only mode This mode runs on a single type of sample, e.g. the tumor or the normal. To create a PoN, call on each normal sample in this mode, then use CreateSomaticPanelOfNormals to generate the PoN.
gatk Mutect2 \ -R reference.fa \ -I sample.bam \ -O single_sample.vcf.gz
To call mutations on a tumor sample, call in this mode using a PoN and germline resource. After FilterMutectCalls filtering, consider additional filtering by functional significance with Funcotator.
gatk Mutect2 \ -R reference.fa \ -I sample.bam \ --germline-resource af-only-gnomad.vcf.gz \ --panel-of-normals pon.vcf.gz \ -O single_sample.vcf.gz