Saturday, April 30, 2011

dbSNP 132 now at UCSC Genome Browser: important changes.

dbSNP 132 now at UCSC Genome Browser: important changes:

While we were traveling for workshops the other day, there was an announcement from the UCSC Genome Browser team that a lot of people have been waiting for: dbSNP132 can be explored on the browser now. It is available on the hg19 assembly–which is the February 2009 one that you can select in the human genome gateway options.

People were eagerly awaiting this for a couple of reasons–first, a new dbSNP release is always offering new SNPs people might want to explore. But this particular release also has SNPs that people wanted to access from the 1000 Genomes project. Here’s the release announcement from dbSNP that describes it:

  1. Build 132:Human include data from 1000 Genomes project pilot 1, 2, and 3 studies.   All 1000 genomes submissions to dbSNP can be searched by batch or using Entrez search filters….

Note: the dbSNP announcement also offers help on filtering for just those SNPs at NCBI if you want them. This led me to try to filter the 1000Genomes submitter name in the UCSC Table Browser as well. It worked–but I haven’t checked all of it yet, so caveat lector on that right now…But some people might want to do that. You could create a 1000Genomes custom track with that sort of query I think.

Table Browser, Filter for dbSNP submitter field:

And this yielded this sort of output–where the submitter field contains 1000Genomes, but it may also include other submitters:

But another really important aspect of the 132 build in the context of the UCSC Genome Browser is that they have changed the way they are offering the SNPs to you. In the past the SNPs have always been in one big bucket. But now they have separated them out into 4 options: Common SNPs, Flagged SNPs, Multiple location mapped SNPs (Mult. SNPs), and All SNPs. So the menus on the browser look like this now:

Key point: the Common SNPs are on by default. If you want All SNPs (or any of the others) you will have to specifically make that choice. Also remember in your table browser queries to make the appropriate selection.

This is a nice option that people have been asking for. But it does represent a change from the way they have been offered before, so be sure you know which SNP subset you want to explore and make the right choice.

PS: I was going to make a custom track of 1000Genomes to load up for anyone as a public service, but I crashed the browser. I may try again later. I think it would be a handy track to have to load up. If someone else gets to it first, let me know and give me your session link and I’ll add it.

PPS: If you don’t know how to navigate around UCSC, change the menu options, or do Table Browser queries, check out the tutorials that we have that are sponsored by UCSC and are freely available:

(Via The OpenHelix Blog.)