Question: VCF file (annotated with snpeff) to MAF
0
gravatar for JJ
24 months ago by
JJ530
JJ530 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 • 1.2k views
ADD COMMENTlink modified 9 months ago by tsy199009290 • written 24 months ago by JJ530

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 24 months ago by _r_am32k

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 24 months ago by JJ530
0
gravatar for tsy19900929
9 months ago by
tsy199009290 wrote:

https://github.com/tsy19900929/snpeffToMaf

ADD COMMENTlink written 9 months ago by tsy199009290
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