[ensembl-dev] Polyphen/SIFT/Condel

[Fiona Cunningham]

Dear Hardip,

Yes it works also on novel variants so it should be able to help you out.

Best wishes,
Fiona

-----------------------------------------------------------------------------------
Fiona Cunningham
Ensembl Coordinator, Ensembl Variation Project Leader.
EMBL-EBI, Genome Campus, Hinxton, UK
www.ensembl.org || www.lrg-sequence.org
fiona at ebi.ac.uk   || t: +44 1223 494612



On 16 April 2012 07:50, Hardip Patel <hardip.patel at anu.edu.au> wrote:
> 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
>
> cheers
>
> 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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