linking GATK to MUTECT

Question

[Bogdan]

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

[Bogdan]

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

[Sean Davis]

You'll need to read the documentation.

Answer 1

[Sean Davis]

The mutect download page is here.

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