I would like to ask about a potential analysis using mutect2 which I am not too sure about please
If you are investigating somatic mutations in a tumour sample using targeted gene sequencing methods (e.g. looking at 30 cancer-related genes using PCR-based targeted sequencing) rather than whole exon sequencing or whole genome sequencing, is it still required to have a matched normal sample if only a very small proportion of normal samples (e.g. <1%) is expected to possess a germline mutation for each gene of interest in our panel?
A possible argument that could be made is that because the expected rate of (deleterious) germline mutations is so low, the matched normal would remove in total very few germline mutations mislabelled as somatic - and therefore there would be no/little need for a matched normal during somatic variant calling using tools such as mutect2.
I would be happy to hear any thoughts regarding this. Thank you in advance.
Please sign in to leave a comment.