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What resource data files are needed for running MuTect?
Please note that this article refers to the original standalone version of MuTect. A new version is now available within GATK (starting at GATK 3.5) under the name MuTect2. This new version is able to call both SNPs and indels. See the GATK version 3.5 release notes and the MuTect2 tool documentation for further details.
MuTect uses the following resources:
General resources (not specific to cancer) such as reference sequence, dbsnp information, etc. can be found as part of the GATK resource bundle. Note that this only includes human genome resources at this time.
The COSMIC files referenced in the Nature Biotechnology publication are available as:
dbSNP files references in the publication are available as: