Question: Pathogenic predictors for Drosophila variants?
1
gravatar for david.rinker
14 months ago by
david.rinker10
United States
david.rinker10 wrote:

Coming from a human genetics background, I have been spoiled for all the ready made tools I have to feed a list of variants into and get effect predictions out (PolyPhen2, CADD, SIFT, etc).

Are there any similar tools for Drosophila? I have a list of ~10,000 variants I'd like to score/rank by some prediction of pathogenicity.

Thanks for any suggestions.

variants drosophila genome • 319 views
ADD COMMENTlink modified 14 months ago by Denise - Open Targets5.1k • written 14 months ago by david.rinker10
2
gravatar for Denise - Open Targets
14 months ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.1k wrote:

Ensembl Metazoa does provide the Variant Effect Predictor (VEP) for fruit fly. You can use the online version (if your 10K variants are less than 50MB) or their Perl script. There used to be REST API endpoint for the VEP in Ensembl Genomes, so it should work for Drosophila. Be aware though that now there is a joint REST server for Ensembl and Ensembl Genomes in Ensembl 96.

Happy VEPing.

ADD COMMENTlink modified 14 months ago • written 14 months ago by Denise - Open Targets5.1k

Thank you. My bad for not adding that I have already run VEP (and snpeff). While VEP output is useful it doesn't distinguish (for example) between conservative and non-conservative amino acid substitutions. I think it looks like my next best step is to generate PhyloP scores via the PHAST package.

ADD REPLYlink written 14 months ago by david.rinker10
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