Entering edit mode
5.7 years ago
wenbinm
▴
40
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!
