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Question: GATK pipeline / Mutect
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gravatar for Bogdan Tanasa
3.0 years ago by
Bogdan Tanasa • 20
United States
Bogdan Tanasa • 20 wrote:

Dear all,

could someone recommend a good resource (possibly a LINUX shell template) for linking GATK and MUTECT in order to call somatic mutations in cancer samples ? many thanks,

 

bogdan
mutect gatk • 1.2k views
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modified 3.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.0 years ago by Bogdan Tanasa • 20
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gravatar for Jennifer Hillman Jackson
3.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

GATK is wrapped for Galaxy, but MUTECT is not (yet). This could be done if you have programming resource. Or, use GATK in Galaxy then download output and use line command. 

Source for MUTECT: https://github.com/broadinstitute/mutect

Best wishes for your project, Jen, Galaxy team
ADD COMMENT • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k
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