Hello. I am using MutCigCV and I am getting some errors (Bellow). My mutation file(MAF file) did have both gene and Hugo.. column but I removed gene column and tried to run MutSigCV again and I got the same error. The MAF file doesn't have any column called patient and none of the patient IDs has "-". So the errors 2, 3 and 5 really don't make any sense.
About chr_file there was no place to include this file that I have downloaded from the website but there is a part that I selected hg19 as reference. I can not figure out why I am getting all these errors. I appreciate it if someone can give me some clues about these. Thank you.
1- unable to perform category discovery, because no chr_files available.Will use two categories: missense and null+indel.
2- Both "gene" and "Hugo_Symbol" are present in mutation_file.
3- Both "patient" and "Tumor_Sample_Barcode" are present in mutation_file. Using "patient".
4- 989/4136 gene names could not be mapped to coverage information. Excluding them.
5- NOTE: Converting "-" to "_" in patient names.