Reformat 23andMe Data for SeattleSNP

Step #1: Download Raw Data from 23andMe

• After signing into 23andMe, first go to "Account" (in the top right hand corner of the screen) and then "Browse Raw Data"
• Click the link near the top of the page to "download raw data"
• Choose "All DNA" for your data set, and then click "Download Data"

Step #2: Reformat Raw Data

• Download the perl script 23andMe_to_SeattleSNP.pl
• There is one parameter that you need to enter:
• genome = raw data file from 23andMe
• PC Users
• Open a terminal window (type "cmd" in Run, for example)
• Move to the folder where your 23andMe data is saved.
• Basic commands:
• cd = change folder
• For example, If the data is in your D:\ drive, you can type "cd \d D:"
• .. = move up one folder
• Type in "perl 23andMe_to_SeattleSNP.pl" and enter the required genome parameter. See example below  (click to enlarge) .

• Mac Users
• Open Terminal (in Applications/Utilities, for example)
• Basic commands:
• cd = change folder
• .. = move up one folder
• Type in "perl 23andMe_to_SeattleSNP.pl" and enter the required genome parameter. See example below (click to enlarge).

Step #3: Upload Data to SeattleSNP

The 23andMe SNP data currently uses NCBI 36 / hg18.  You can confirm if this is still the case by using a text editor like Notepad++ to view the raw data.

There are a few different portals to access SeattleSNP annotations, but you will need to use this link if the 23andMe data is currently using NCBI 36 (as of today, NCBI 37 / hg19 is the latest genome build): http://snp.gs.washington.edu/SeattleSeqAnnotation/

• Enter your e-mail address
• Select the file created by the perl script.  It should be almost identical to the genome file, but it will say _SeattleSNP.txt at the end of the file
• This file conforms to the "custom" format, so please select "custom" under "input file format" and enter the following information
• Chromosome: 2
• Location: 3
• Reference Allele: 0
• First Allele: 4
• Second Allele: 5
• Click the green submit button
• It may take several hours to annotate your 23andME SNPs.  You will recieve an e-mail message when the annoted file is ready to download.

I have tested my perl scripts on a PC and Mac, but I cannot guarentee that they will work on every possible platform.   Also, these scripts may need modifications as file formats change, but I have currently confirmed that my scripts work with v2 and v3 arrays using genomes from Genomes Unzipped.  If you have any questions or comments, please post them below and I will do my best to help troubleshoot.