About the MAF file

sibscc

Some downstream analysises need an MAF (mutation annotation format) file.
Can TCGA or other realted tools annotate the vcf files and reformat them into MAF format?
Another little question, I can't get any search result by the box upright. It always lets me go to the guide, although I am trying to find key words already mentioned in the forum.
Thank you.

Geraldine_VdAuwera

Hi there, sorry for the delayed response. I think Oncotator (see here) may do what you want, if I understand your question correctly.

Re: the search box, can you tell me what keywords you tried?

sibscc

Thanks for your reply.
Oncotator may be my solution, will try it.

Say search "Oncotator", get nothing.

Geraldine_VdAuwera

See the Oncotator docs here: http://gatkforums.broadinstitute.org/categories/oncotator