To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

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 is good enough? There is the big problem!

Thank you for your help.


  • shleeshlee CambridgeMember, Broadie, Moderator

    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:

    What is the big problem?

Sign In or Register to comment.