1000 genome variants

[johnadam33]

Now with 1000 genome information integrated into the Ensembl browser, does any one know how one can get the information for a list of chromosome locations? I have thousands of chromosome locations that I want to see if they are already included in 1000 genome data as SNPs. I can do individual location, but is there a simple way one can upload them and see. Its fine if its only for few hundreds. I can split the file into small ones of few hundreds each.
Thanks.

[Jorge Amigo]

1000 genomes usually releases a list of variant sites they found (as for the current version, this file could be retrieved from here), which can be queried by a self made comparison script to check your variants existence in it.

what I usually tend to do for this kind of simple batch queries, specially when population genetics is involved, is to use our tool ENGINES and batch search there what I need. it's not as powerful as other sites, but does solve plenty of our daily variational concerns.

[johnadam33]

Thanks a lot Amigo. The problem I have is that I am new to this and have no programming skills. I can't write scripts. I use to check individual varinats with 1000 genome browser, but I am now having more than thousand to check for SNPs in 1000 genome database. I hope there be a simple solution.

[Jorge Amigo]

a great tool we also use is ANNOVAR, which is able to provide you with a local copy of the latest updates of some major variant databases, including dbSNP132 or 1000 genomes. I would go for that first, since it works like a charm once you have all those databases on your disk (it downloads them for you, so it is pretty simple).

if you still want to go for our tool you will have to have in mind that we currently support previous 629 samples release (we are about to update it with the recent 1094 batch), but you can try copying and pasting your individual variants in chr1:123456 format in ENGINES search box and see if it is able to deal with them. let us know if you have any problems.