Mutsig crashes with error "matrix dimensions must agree"

[kbrar4013]

Hi,

I'm using MutSig2CV on a Linux platform using the 64-bit executable with MATLAB 2013a runtime installed. I've attached the output of the tool below; it crashes with error "matrix dimensions must agree". Also, it's detecting "newbase" as a column, but this isn't actually a named column in my file. Any ideas on what might be going on here and what I can do to troubleshoot this?

[julianhess]

Hi,Looks like your MAF is malformed—there seem to be blank chromosomes, and a chromosome named “Chromosome,” suggesting that multiple TSVs have been catted together without removing headers in between.The newbase column gets added implicitly, and is not something to be concerned about.—JulianOn Nov 11, 2023, at 13:23, Karanbir Brar @.***> wrote: Hi, I'm using MutSig2CV on a Linux platform using the 64-bit executable with MATLAB 2013a runtime installed. I've attached the output of the tool below; it crashes with error "matrix dimensions must agree". Also, it's detecting "newbase" as a column, but this isn't actually a named column in my file. Any ideas on what might be going on here and what I can do to troubleshoot this?

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[kbrar4013]

Hi, thanks so much for your response. I'm editing my MAFs to remove all chromosomes that aren't 1-21, X, Y and running the tool with a MAF file that only includes 5 patients, just as a test to get the tool working. I'm now running into a different issue, as you can see below: it looks like there is an error for every gene with the error "Operands to the || and && operators must be convertible to logical scalar values". Would really appreciate any help you can provide - thanks again!

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[julianhess]

Can you please post an excerpt of your MAF? Sounds like there are some other problems with the mutation data.