Tip of the Week: SNPTips and viewing personal genome data

Today’s tip of the week is on SNPTips. We had a guest post on this earlier. We usually do tips on databases and analysis tools, but after getting our 23andme data, we’ve been using SNPTips often and thought it might be of use to some of our readers. SNPTips was created by 5am Solutions for 23andme* customers to easily view their genomic data while browsing the web. The tip will quickly show you how to install the browser extension and what it does. At the end of the tip, I  briefly show a custom annotation track I created of my 23andme data using UCSC Genome Browsers** Personal Genome SNP format.  The format is not perfect for 23andme data (doesn’t allow for rsID field, has fields of little use with 23andme data, etc), but it does help tremendously if you want to browse your data with the genome browser. You basically take the 23andme data that looks like this:

and rearrange the columns, add a few to make it look like this:

You can do this in a spreadsheet program like I did, it’s a bit labor intensive. If I decide to do it for my daughter’s and husband’s genome data (which is a distinct possibility), I’d created a perl script to change the format (or maybe there is something already out there?).

It basically entails:
*eliminating the  rsID column
*rearranging the columns to the correct order
*adding “chr” to the chromosome number
*adding four columns, 1 with the number of alleles, 2 with 0′s (frequency data the 23andme data doesn’t have)
*changing the genotypes from xx to x and xy to x/y.

Remember also that the 23andme position data is from build 36 (2006, hg18) and the genotypes displayed in 23andme data are oriented with respect to the positive strand on the reference assembly.

It’s not the most elegant solution, but it works and nicely with SNPTips. It has been quite addictive for me :). I’m sure there are more elegant ones that can be done.

*OpenHelix and it’s employees have no commercial connection or financial interest with 5amsolutions or 23andme.
**UCSC sponsors tutorials and outreach with OpenHelix through as a subgrantee.

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