Question: GATK pipeline / Mutect
0
gravatar for Bogdan Tanasa
2.4 years ago by
United States
Bogdan Tanasa20 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 • 1.1k views
ADD COMMENTlink modified 2.4 years ago by Jennifer Hillman Jackson24k • written 2.4 years ago by Bogdan Tanasa20
0
gravatar for Jennifer Hillman Jackson
2.4 years ago by
United States
Jennifer Hillman Jackson24k 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 COMMENTlink written 2.4 years ago by Jennifer Hillman Jackson24k
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