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How to optimise parameters for sequencing at higher depths?


I have a targeted bait panel that covers approximately 350Kb, our plans are to sequence tumour libraries to approximately 1200x post deduplication, we do not have a matched normal. The high depth is in order to detect rare variants.

Do you have any advice on which parameters within Mutect2 (tumour-only mode) and FilterMutectCalls that should be tweaked not only to take into account the lack of a matched normal but also the extreme depth of sequencing?

Any advice would be greatly appreciated.


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