[ensembl-dev] getting watson snps

Andrea Edwards edwardsa at cs.man.ac.uk
Mon Dec 13 17:05:35 GMT 2010


Hello

I received an email saying ebi would make wastons snps available as dump 
filesin the next release

The dump files would be great but I am also retreiving lots of other 
information about the snps with the snps and that might not necessarily 
be in your dump file so i think i have to try other options too.

This is what i have tried so far to get the watson snps and not getting 
anywhere fast :)

1. Written perl script to download them from ensembl human variation 
database. This works but will take over a month to get all the snps at 
the rate at which it seems to be running and i imagine you'll block my  
ip address if i leave it running :) Plus I can't leave it a month anyway.

2. I've tried to install the human variation database locally but that 
also seems to be having problems. It has been installing the allele 
table now for 3 days i think. It is running on a very slow machine but 
there are far bigger tables than the allele table so i dread to think 
how long they will take. I tried to get access to a better machine but i 
wasn't give enough hard disk space but perhaps that will solve the 
problem! How long should it take to install the human variation database 
(roughly) on a 64 bit linux machine with 2 gig of ram and intel xeon @ 
2.27GHz? Will it take hours or days?

Is there anything else i can try. I do appreciate that the dataset is 
vast and these things will be slow? Perhaps the answer is simply a 
faster machine to install the local database and I am looking into this.

I have already looked at getting the snps from dbsnp or directly from 
source but i need to get information associated with the snps so will 
have the same problems i think of retreiving the associated data even if 
i got the 'raw snps' by other means

Many thanks




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