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RNA-seq and WGS for cancer samples (no paired T-N)
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.