identify mutations in RNAseq data


I have 4 tumours samples and 4 matched controls. I would like to know if there are mutations present in all 4 tumour samples that are not in the controls. So far, I generated BAM files with HiSat2 and then ran VanScar on those BAM files. Now I have 4 files comparing each pair but I’m not sure what I’m supposed to do next.
Thanks for your help

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Hi @delphine

Please see the tutorials here: