search

evenrus / mmsig

A method for fitting a known mutational signature reference to mutational catalogues from cancer samples
Other
7 stars 5 forks source link

Error while using hg38 #5

Open parvathisudha opened 7 months ago

parvathisudha commented 7 months ago

Hi,

I am trying to use mmsig on the WGS data. My files are in hg38. I am using COSMIC (v3.2) GRCh38 SBS as the reference file. I have also set refcheck = FALSE. Even then, few snvs are not recognized by the program. Code: smm_sig_outhg38 <- mm_fit_signatures(muts.input=snvs, sig.input=sig_ref_hg38, input.format = "vcf", sample.sigt.profs = NULL, strandbias = FALSE, bootstrap = TRUE, iterations = 20, refcheck=FALSE, cos_sim_threshold = 0.01, force_include = c("SBS13","SBS2"), dbg=TRUE) Error: Error in .Call2("C_solve_user_SEW", refwidths, start, end, width, translate.negative.coord, : solving row 36159: 'allow.nonnarrowing' is FALSE and the supplied start (78180144) is > refwidth + 1

Do you recommend to change any other parameters here while running the program for hg38 reference?

Thanks! Parvathi.

kunstner commented 3 months ago

Did you find a solution to the problem? I'm running into the same issue. Probably, one has to perform a liftover to hg19.

edit: I forked the project and adjusted the code for GRCh38 (https://github.com/kunstner/mmsig)