MutSig2CV with self-generated "maf file:

Question

[sitapriyamoorthi]

Hello All, I am trying to run MutSig2CV with a MAF file that I generated from an excel file. I used the correct case and terms to generate the maf file and I get the following error! Any advice would be great!

Mutation file is missing a column named one of the following: gene Hugo_Symbol Gene_name Error using MutSig_2CV_v3_11_core (line 169) Mutation file missing gene column.

Error in MutSig_2CV_v3_11_wrapper (line 50)

[bari.ballew]

It sounds like MutSig2CV is looking for, but not finding, a gene name column called either "gene," "Hugo_Symbol," or "Gene_name." Can you show us the first few lines of your input file?

Answer 1

[sitapriyamoorthi]

chr pos gene patient ref_allele newbase type classification 6 30545853 ABCF1 T10146-B1 CA C Frameshift c.218delA 6 30545853 ABCF1 T11547-E1 CA C Frameshift c.218delA 6 30545853 ABCF1 T16419-E2 CA C Frameshift c.218delA