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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!



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