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MutSigCV-errors-Gene, patient, chr_file

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.
genome software-error
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updated by Ram Ram • written by Arton • Arton

I'm having more or less the same issues. Based on my outcomes:

For 2 I'm assuming the tool refers to the coverage file versus maf and therefore it selects "gene" to the final output

4- as the message indicates the maf file contains 9xx genes which do not exist in the coverage file

1 and 3 are my problems too, but I'm trying to change the content of the maf file to observe when this message might disappear.

hth!

• 1 views • link
updated by Ram Ram • written by H.Hasani H.Hasani

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