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MuTect and SomaticIndelDetector

mikemike Member
edited October 2012 in Ask the GATK team

Hi, Dear Kristian Cibulskis:

Sorry. I just saw this comments above and re-posted my questions here about MuTect:

Just a few questions about MuTect, which I was confused or not so clear based on GATK documentation

Is the MuTect is the same as the so called SomaticIndelDetector in GATK 2.0 as described at the following URL; (I felt they are different, just want to confirm)
http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_indels_SomaticIndelDetector.html

If they are different, how to access the MuTect from GATK using -T option or other methods, or we have to follow the following URL as mentioned above to download?
https://confluence.broadinstitute.org/display/CGATools/MuTect

Thank you for your help!

Mike

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