This next post in our continuing semi-regular Guest Post series is from Andrew Johnson, one of the developers and the concept designer of SNAP, SNP Annotation and Proxy Search which is hosted at the Broad Institute. If you are a provider of a free, publicly available genomics tool, database or resource and would like to convey something to users on our guest post feature, please feel free to contact us at wlathe AT openhelix DOT com or the contact form (write ‘guest post’ as subject heading). We welcome introductions to your resource, information on updates, highlights of little known gems or opinion pieces on the state of genomic research and databases.
SNAP (http://www.broadinstitute.org/mpg/snap/, Johnson et al. (2008) Bioinformatics 24(24): 2938), “SNP Annotation and Proxy search”, is a flexible, web-based tool that allows anyone in the world to quickly accomplish a range of SNP-related genetics and bioinformatics tasks. This post highlights some common questions andfeatures of SNAP, some more obscure uses, and recent and planned developments.
How did SNAP come about?
The idea for SNAP was originally sparked by GWAS analysts within a large collaborative group (the Framingham Heart Study SHARe project). This was in the pre-imputation era when GWAS investigators from different groups using different SNP arrays often wanted to find best proxy SNPs based on HapMap for comparison when they didn’t have common genotyped SNPs across groups. We initially implemented local programs to lookup upHapMap LD and also consider the presence of query and proxy SNPs on different commercial genotyping arrays. We quickly realized this was a community-wide problem as we received requests from outside collaborators so we decided it was worth developing a public tool and approached investigators at the Broad Institute. Through collaboration with Paul de Bakker, Bob Handsaker and others at the Broad Institute we were able to add more features like plotting and build a nice, quick and accessible interface. Many people have contributed ideas, testingand improvements to SNAP, and Bob Handsaker and Pei Lin in particular continue to maintain and update SNAP.
What do you use SNAP for the most?
The two major features of SNAP widely used 1) SNP LD queries, and 2) plotting of LD and association data. There are a number of flexible options for these functions. Beyond these, as a SNP bioinformatics specialist, I often use SNAP to rapidly retrieve information about a list of SNPs for other uses (see specialized queries below).
What are some commonly asked questions from users of SNAP?