MutSig coverage table
1
1
Entering edit mode
9.5 years ago

Hi everyone,

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!

Sadiq

mutsig coverage wig • 4.0k views
ADD COMMENT
0
Entering edit mode

Hi Sadiq, Have you tried mutect to generate such a coverage file? BTW, I am searching the same answers. Would you share your solutions if you have one? Thanks Shirley

ADD REPLY
0
Entering edit mode

Hi Sadiq I came across the same error. I am thinking that may because I used the non-synonymous mutations only. because according to the "mutation_type_dictionary_file", only silent and synonymous mutations are classified as "silent". thus in my data, there are no silent mutations. right now i'm trying to add the synonymous data back, but keep using the exome_full192.coverage.txt what do you think? do you have any suggestions? thank you!

April

update: i did what i mentioned above: adding the synonymous data back. then i ran MutSig successfully and got the data i want

ADD REPLY
0
Entering edit mode

Hi Shirley and April - Sorry I have not used this tool for many years now. I think I am not the best person to answer this question. Apologies. Wish you all the best

ADD REPLY
0
Entering edit mode

No problem. I added the synonymous mutations back and it worked. So make sure the input file includes both synonymous and nonsynonymous mutations.

ADD REPLY
1
Entering edit mode
6.6 years ago

CovGen can help make a capture/target specific coverage file. However, your error is most likely caused by how you filter your variants before going into MutSig.

ADD COMMENT
0
Entering edit mode

Could you please tell me how to use CovGen?The documentation on the GitHub is too brief and I can't understand.I will be very grateful´╝ü

ADD REPLY

Login before adding your answer.

Traffic: 848 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6