[ensembl-dev] variation database usage

Hardip Patel hardip.patel at anu.edu.au
Thu Feb 16 10:21:38 GMT 2012

Dear all

I have vcf files generated for individual chromosomes from a human resequencing project. I was wondering if somebody could get me started with ways to use the variation api.

I am mainly interested in knowing following from my vcf files.

Is the variation in vcf is found in dbSNP and if yes, is it the same genotype as the one in my vcf file?
Is the variation implicated in NHGRI_GWAS catalogue or not?

I have tried reading documentation on variation api and i am not able to come up with a way to do this. 

I am able to use parse_vcf subroutine to parse vcf line and get a variation feature object. I am getting stuck after that in that I am not sure how to use the variationfeature to ask the above questions.

Any help is greatly appreciated.

Kind regards

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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