The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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.