Generate new maf file

Hi

I'm trying to use MutSigCV but so far have no luck trying to make the MAF mutation table from VCF and annovar files.

I'm not using TCGA data so the python tool that converts VCF to MAF doesn't work for me.

I'm wondering if there is a tool/script for that purpose?

Thanks!

Variant_Classification

Hi,

Thanks for the response to my previous post.

On a related note, how did you get the Variant_Classification field?

Thanks,

VCF to MAF

Although in principle a VCF to MAF converter shouldn't be hard to create, I am not aware of a general purpose script to do this. You may be able to use our Oncotator tool to go from a list of mutations to a MAF file.

questions about 'categ'

Thanks for the reply. I read the user manual but I guess my question is how to generate the 'categ' part, specifically, how do you define CpG transitions as distinguishable from say a C:G transition in the context of GCG.

categ

To run MutSigCV, first generate the MAF file that omits the categ and effect columns. Then, follow the instructions under "Running MutSigCV when all you have is a MAF file."

To answer your specific question, if a G is on the 3' end of a C, then it falls into a CpG category. And, if a C is on the 5' end of a G, then it likewise falls into the CpG category. If some other base is on the 3' end of a C (in the first case), or on the 5' end of a G (in the second case), then it falls into a non-CpG other category.