Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
How to create a coverage table for MutSig?
I am trying to use MutSig and would like to know if there is a way/script to generate coverage tables for the experiment under analysis. I have tried to use the standard exome_full192.coverage.txt file provided by Broad Institute but I run into the following error:
silent and nonsilent rates are too different
I guess I will have to create my own coverage tables. I have searched various forums thoroughly including Biostars but so far I haven't been able to find a solution. I will very much appreciate if the folks on this forum, who have some experience with MutSig, can help me out.
Thank you so much!