Hi all. I am trying to use GATK Mutect2 to do somatic variant calling. Not like VarScan Somatic, which allows the user to input normal and tumor bam files. Mutect2 only has one input field. I read through its example but still found nowhere to input the paired bam files. Can anyone help me on this issue? Thank you ahead.
gatk Mutect2 \ -R reference.fa \ -I tumor.bam \ -I normal.bam \ -normal normal_sample_name \ --germline-resource af-only-gnomad.vcf.gz \ --panel-of-normals pon.vcf.gz \ -O somatic.vcf.gz