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MuTect v1 or Mutect v2?

bernard2aral159bernard2aral159 FranceMember

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.

Answers

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @bernard2aral159,

    Where did you download the COSMIC resource file from? I recommend using resources that we provide in our bundle to rule-out file format issues. If these resources are still causing an error, then please post the exact MuTect command you are using.

    Here are some general guidelines to follow:
    image

    What is the big problem?

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