Conversion of variant data

Question

[sherinmolthomas85]

I need to analyze the variant data generated from jbrowse in SNPEff. I usually retrieve variant data in ggf3 format and make a text file out of it. The outputs from SNPEff using text file is not making any sense(It gives no protein change always).

[Devon Ryan]

I've never heard of anyone actually calling variants with JBrowse. Are you sure that's what you mean? Also, GFF3 is not a standard format for holding variant data, that's what VCF is for.

Answer 1

[Bert Overduin]

As already indicated by Devon, the standard format for variants is VCF format, which is the input format for most, if not all, variant annotation tools. However, if you want to use another format, you could have a look at the Ensembl Variant Effect Predictor. The VEP also accepts formats other than VCF, e.g. a default format, which you should easily be able to create from your GFF3 file. The VEP is available through a web interface, as a downloadable script and also through the Ensembl REST API. Of course it only works for those genomes that are part of either Ensembl or Ensembl Genomes.

[sherinmolthomas85]

Thanks Bert