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MuTect v1 or Mutect v2?
Hi! I downloaded the cosmic file b37_cosmic_v54_120711.vcf, but still I had an error after running MuTect v1. Should I still go through liftover and filtering process this later file? Or best, I am using GATK v3.5 where MuTect v2 is included, then is just using the coding mutants Cosmic vcf from cancer.sanger.ac.uk/cosmic/download is good enough? There is the big problem!
Thank you for your help.