Question: VCF to maf
0
gravatar for fabbri.marco
9 months ago by
fabbri.marco0 wrote:

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

conversion maf vcf • 374 views
ADD COMMENTlink written 9 months ago by fabbri.marco0

I had problem to install

We need more details, error/warning messages.

ADD REPLYlink written 9 months ago by zx87549.9k

My question was on possible alterative tools.

ADD REPLYlink written 9 months ago by fabbri.marco0

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 --pick flag (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.

ADD REPLYlink written 9 months ago by Amitm2.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 928 users visited in the last hour