The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
Use TCGA variants instead of COSMIC
I am wondering about the possibility to use TCGA variants instead of cosmic in MuTect. Given that it's mostly used to upweight positions that are in dbSNP AND cosmic I think this would be a smart move. Cosmic seems like a mess, with small single-gene experiments mixed with larger experiments. The TCGA pancan MAF seems way mor structured. My guess is that most dbSNP somatic variants are so common that they will be in TCGA pancan as well.
Has anyone tested this or have experience with it?
(my basic plan is to convert TCGA pancan MAF to VCF and use in MuTect).