Want to Skip Annotation Step (in MutSig_preprocess)

Question

[Charles Warden]

I am trying to run MutSig with with the three minimal input files (and output path):

MutSigCV('mutations.maf','coverage.txt','covariates.txt','output.txt')

However, I am getting the following error message:

======================================
  MutSigCV
  v1.4

  (c) Mike Lawrence and Gaddy Getz
  Broad Institute of MIT and Harvard
======================================


MutSigCV: PREPROCESS
--------------------
Loading mutation_file...
Loading coverage file...
Processing mutation "effect"...
Error using MutSigCV>MutSig_preprocess (line 291)
missing mutation_type_dictionary_file**

Error in MutSigCV (line 184)
  MutSig_preprocess(mutation_file,coverage_file,covariate_file,output_filestem,varargin{:})

------------------------

I would expect this error if I had entered additional parameters (when you only have a .maf file), but I am trying to follow the instructions as provided on this website:

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

Does anyone know how to fix this problem? I guess I can change the source code, but I was hoping that there was a simpler solution. Or, if you have contact information for a MutSig support team, then that would also be helpful.

[Charles Warden]

FYI, it wasn't that hard to skip the pre-process step in the source code (and avoid renaming the files for the second step). So, that is how I fixed the problem. I'll leave the question up, just in case somebody has a better suggestion. For example, I wouldn't have been able to do this without a MATLAB license.

Answer 1

[Charles Warden]

For those that didn't already know, there is a Help Forum for CGA Tools (which includes MutSig):

http://www.broadinstitute.org/cancer/cga/forum/5

[Max]

I'm having the same problem running MutSigCV (i.e. line 184 error when calling MutSigCV(mutationfile,coverage,covariates,output,dictionary,chr19ref) ). Would you mind providing me with some more detail about the hack that proved to be a successful work-around for you? From your description, it seems like you just deleted/commented out the pre-processing step in the MutSigCV .m script, is this correct? If so, was there any change to the arguments provided to the MutSigCV call?

Thank you.

[Charles Warden]

Unfortunately, I no longer have access to that code (or a MATLAB license). Sorry about that.

Answer 2

[fongchunchan]

I went with the approach of only using only the MAF file approach downloading the 4 references files and it worked for me. Have you tried that?

Were you able to get it working? I am interested in trying to figure out how to build a coverage file for my dataset, but still have the pre-processing step determine the "categ" and "effect columns for me.

[Charles Warden]

Yes - I was able to get the script to work eventually, but I was not very pleased with the results (perhaps because I only had tumor samples and was trying to approximate somatic mutations using filtering methods).

My scripts would probably be comparable to what someone could produce with some moderate python or perl programming experience (and would probably not be the most efficient way to write code when considering a large number of genomic positions). That said, the solution to my original post was relatively simple (the pre-processing code is a function that can be easily skipped), compared to the code to create the coverage file on my own.

I am no longer working on this project, so I apologize that I cannot be more help. Good luck!