Mutect2 (doc)
call somatic SNPs and indels.
This wrapper is largely inspired by this wonderful tutorial on Mutect2.
- Tumor-only (usually used to create PoN)
- {sample}.bam, reference -> {sample}.vcf.gz
- Tumor-normal
- {tumor_sample}.bam, {normal_sample}.bam, reference -> {tumor_sample}.vcf.gz