Using Mutsigcv to analyze COSMIC data

Question

[wenbinm]

Hi there.

Has anyone tried analyzing COSMIC data using Mutsigcv? This is what I did: I downloaded vcf file from COSMIC and used package VariantAnnotation to load it into R. Then I typed

cosmic_sub_data = cosmic_data[which(rownames(cosmic_data) %in% brca_mut_list$MUTATION_ID)] writeVcf(cosmic_sub_data,'Cosmic_brca.vcf')

to subset breast cancer data. After this I used https://github.com/mskcc/vcf2maf to get maf file (during this I got the same error and fixed as in https://www.biostars.org/p/328659/). Then I upload to Mutsigcv and got an error like:

Error using gp_MutSigCV>MutSig_runCV (line 851) nonsilent mutation rate out of range

Error in gp_MutSigCV (line 194)

Does anyone know what happen?

Thank you!