[ensembl-dev] Polyphen/SIFT/Condel

Hardip Patel hardip.patel at anu.edu.au
Mon Apr 16 07:50:40 BST 2012

Dear All

I have recently used the variation_effect_predictor script with parameters enabled to report both the score and the prediction term from SIFT, PolyPhen and Condel analysis.

I wanted to know if the vep script will report scores of all these programs only if the variation is known or it will also report scores for novel variations that I detect in my dataset. i.e. Does it calculate the scores for novel variations on the fly?

Ultimately, my aim is to use the scores given by VEP script to sort through variations without having to do any additional computation (Condel, PolyPhen, or SIFT analysis on novel variants) on the variations that were not accounted for by the VEP script.

I hope this makes sense and thank you all in advance for responding.

Kind regards

PS: I am using ensembl v66, latest VEP version, and local install of the mysql variation database. I have also downloaded cache from the website and I am running the following command:

variant_effect_predictor.pl --output_file out.vcf --species homo_sapiens --host localhost --user user --password password --port XXXX --db_version 66 --format vcf --buffer 1000000000 --force_overwrite --input_file in.vcf --terms ensembl --sift b --polyphen b --condel b --regulatory --gene --protein --hgnc --ccds --numbers --domains --per_gene --check_ref --check_alleles --cache --no_progress --vcf


Hardip R. Patel, PhD
Post-doctoral Research Fellow

Genome Discovery Unit and RNA Biology Lab
Genome Biology Department
The John Curtin School of Medical Research
College of Medicine, Biology and Environment
The Australian National University
Building 131, Garran Road, ANU Campus, Acton - 0200, ACT, Australia
Email: hardip.patel at anu.edu.au, patelhardip at gmail.com
Phone Number: (+61) 0449 180 715

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