Question: VCF file (annotated with snpeff) to MAF
0
gravatar for JJ
21 months ago by
JJ520
JJ520 wrote:

Hi all,

I've read the posts here on VCF to MAF conversion (e.g. Converting Vcf File To Maf ). However, I could not manage to convert a snpeff annotated VCF file to MAF. Is there any way? Any tool that can do this? or do I need to use VEP for annotation?

Thanks! JJ

sequencing genome • 968 views
ADD COMMENTlink modified 6 months ago by tsy199009290 • written 21 months ago by JJ520

I could not manage to convert

Please be more specific - what happened when you tried? Did you see any error message? What was the message? If there was no message, how did you know you did not succeed?

ADD REPLYlink written 21 months ago by RamRS30k

I am sorry for not being more specific - it's a known issue: https://github.com/mskcc/vcf2maf/issues/174 the converter does not work with snpeff annotated files - hence I was wondering if there is a tool that could do that.

ADD REPLYlink written 21 months ago by JJ520
0
gravatar for tsy19900929
6 months ago by
tsy199009290 wrote:

https://github.com/tsy19900929/snpeffToMaf

ADD COMMENTlink written 6 months ago by tsy199009290
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