Question: linking GATK to MUTECT
0
gravatar for Bogdan
3.4 years ago by
Bogdan740
Palo Alto, CA, USA
Bogdan740 wrote:

Dear all,

as I have just started working in the field of cancer genomics, I was wondering if anyone could 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

gatk • 1.2k views
ADD COMMENTlink modified 3.3 years ago • written 3.4 years ago by Bogdan740
1
gravatar for Sean Davis
3.4 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

The mutect download page is here:

https://www.broadinstitute.org/cancer/cga/mutect_download

You'll need to make an account before being able to access it. 

ADD COMMENTlink written 3.4 years ago by Sean Davis25k
0
gravatar for Bogdan
3.3 years ago by
Bogdan740
Palo Alto, CA, USA
Bogdan740 wrote:

Thanks Sean. Dear all, could I find some TEMPLATE CODE  that will allow running MUTECT on each chromosome (or chromosome fragment) ?

ADD COMMENTlink written 3.3 years ago by Bogdan740

You'll need to read the documentation:

http://www.broadinstitute.org/cancer/cga/mutect_run

ADD REPLYlink written 3.3 years ago by Sean Davis25k
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