[ensembl-dev] variation sets

Will McLaren wm2 at ebi.ac.uk
Sat Oct 23 16:01:09 BST 2010

Hi Andrea,

We use variation sets internally to subset variations into various
categories. One such set, as you say, is called "Phenotype-associated
variations". We also have sets for, e.g. 1000 genomes SNPs and HapMap
SNPs. These sets are only presently used in the human database.

You can find a list of all available sets using the following code:

my $vsa = Bio::EnsEMBL::Registry->get_adaptor("human","variation","variationset");

foreach my $vs(@{$vsa->fetch_all}) {
  print $vs->name, " - ", $vs->description, "\n";

While you could use the code you quoted to retrieve all
phenotype-associated variations, this could take a long time; you
might be better off using BioMart.

Unfortunately without creating your own copy of the variation database
and getting stuck in with some MySQL it would not be trivial to create
your own variation sets.

I'm not 100% clear what you are trying to achieve here; if you are
interested in phenotype-associated variations, you should also look
into the documentation for variation annotations, as this is how we
denote the relationship between a phenotype and a variation.


Will McLaren
Ensembl Variation

On 23 October 2010 13:19, Andrea Edwards <edwardsa at cs.man.ac.uk> wrote:
> Hi
> I don't understand what a VariationSet is in the variation API. One of the
> methods is
> $vg = $vga->fetch_by_name('Phenotype-associated variations');
> Is the parameter 'Phenotype-associated variations' from a list of built-in
> parameter values so that ensembl will go away and retrieve all variations
> associated with a phenotype. If so, what are the other allowable parameter
> values?
> Alternatively this method could retrieve a set of variations that the user
> has somehow created and called 'Phenotype-associated variations' themselves
> (e.g. by uploading the variations into a personal data area perhaps)
> Many thanks
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev

More information about the Dev mailing list