andrej-fischer/emu

An Expectation-Maximization algorithm to infer mutational signatures

emu's Issues

specifying spectra initializations?

Is there a way to provide specific initializations for the spectra rather than defaulting to 10 random starting positions when forcing the number of spectra (Nsp)? Do you have any suggestions on how to add this as an option?

Question regarding using WGS Opportunity

Hi,

I wanted to implement EMu in our pipeline and had a few questions:

1. Whether using '--opp' parameter is required when using the --spectra option?
2. If I would be using any VCF file with Somatic mutations from a WGS sample, and compare it to the COSMIC Signatures using the --spectra option, would I need to use the --opp parameter with human-genome?
3. If I am analyzing Exome samples, and comparing it to the COSMIC Signatures as above, do I need to normalize the input, or use the 'human-exome' opportunities?

Your suggestions are appreciated.
Thanks.

Reference is lowercase

For 1/5 of the mutations, the tool says ERROR: Mutation A>G at position ---- in chr 2 in ---- not possible! Reference is 'a'.

I tried adding middle = toupper(middle) before this check, but now it results in a segmentation fault.

Error running large no. of samples & spectra

Hi,
first off, thanks for the awesome program!

Everything works fine for hundreds of samples, but I'm running into periodic determinant = 0 errors while running EMu with a large number of samples (~6000). [Err msg: In get_llhood for m=6***, det(Hf) = 0.... ]

The program works fine up to ~15 spectra, then such errors start occuring periodically. I am thus unable to run EMu to completion for anything beyond 15 spectra.

Let me know if you need my .mutations or .opp. file.

Thanks!