Dear GATK Team,
I want to do SNP calling on cancer RNA-seq data (no matching normals). In some cases I have matching WGS data (for which I also want to do SNP calling) - but not for most cases.
If I understood this correctly I cannot use MuTect2 without matching normals - so do you then recommend GATK or a completely different tool?
I very much appreciate your help.
Best,
Julia
