Question: Converting VarScan output (.txt) format to .vcf for annotation
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gravatar for ivivek_ngs
5.1 years ago by
ivivek_ngs4.8k
Seattle,WA, USA
ivivek_ngs4.8k wrote:

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

snp varscan2 vcf • 3.9k views
ADD COMMENTlink modified 5.1 years ago by Pablo1.9k • written 5.1 years ago by ivivek_ngs4.8k
0
gravatar for Pablo
5.1 years ago by
Pablo1.9k
Canada
Pablo1.9k wrote:

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

   Annotating Tcga Mafs With The Latest Ensembl Transcripts

Link to his MAF to VCF converter:

   https://github.com/ckandoth/vcf2maf/blob/master/maf2vcf.pl

ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by Pablo1.9k

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?

ADD REPLYlink written 5.1 years ago by ivivek_ngs4.8k
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