Converting VarScan output (.txt) format to .vcf for annotation

Question

[ivivek_ngs]

Dear All,

Is there any script available that will help me to convert the VarScan output in .txt format to .vcf format which I can use to annotate for snpEff. The .txt handle for snpEff seems to be deprecated, so I have want to convert my somatic variants .txt file(normal/tumor) pair to corresponding .vcf file and use for annotation with snpEff. I do not want to run VarScan again to generate the output in .vcf format. It would be nice if anyone can provide me some script or information to do the same.

Thanks

Answer 1

[Pablo]

I recommend taking a look at Cyriac's tutorial (it's very well written)

His MAF to VCF converter

[ivivek_ngs]

Yes but in my case the output is not in MAFs. The output is in text format of the normal varscan output, how do I convert it to MAF format then?