Entering edit mode
3.0 years ago
fabbri.marco ▴ 10
I need to convert a vcf file to maf file. I had problem to install vcf2maf on my old window machine (I am stuck at home for the virus). Any alternative? Maybe an R package. I need since I would like to use maftools. Thank for any suggestion. Best, Marco
We need more details, error/warning messages.
My question was on possible alterative tools.
A couple of suggestions which might be useful - 1) If you are not already using conda, please do so to install vcf2maf. 2) Are you able to get VEP working? If yes, then you could run VEP with the
--pickflag (and tabular data output) so that the output in effect is like vcf2maf. And then you can manually create a MAF format by selecting out the appropriate cols. from the VEP output. I do not know what downstream tool you want to feed the MAF into, but sometimes this strategy works. 3) If you are ok with uploading your variant list on public server, you could run the VEP part online; there is a limit though on the no. of variants you could upload in one go.