Summarize 23andMe SNP Categories

The primary goal of this script is to provide statistics about your 23andMe SNPs (number of annotated SNPs, number of homozygous / heterozygous disease assocations, number of coding SNPs, etc.)


Step #1:Create a 

• Prepare combined SNP file (click here for details)
• This will also work for filtered files (check here for details)

Step #2: Produce Summary Statistics

• Download the perl script 23andMe_stats.pl
• There is one parameter that you need to enter:
• inputfile = file containing 23andMe SNPs with both SeattleSNP and GWAS Catalog annotations (click here for details)
• 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
• If the data is not in your C:\ drive, you can type "cd \d D:"
• .. = move up one folder
• Type in "perl 23andMe_GWAS_stats.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_GWAS_ stats .pl" and enter the required genome parameter. See example below  (click to enlarge) .

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.