Filter Combined Annotations for 23andMe SNPs

Step #1: Prepare Inputfile

• List of 23andMe SNPs with both SeattleSNP and GWAS Catalog annotations (click here for details)

Step #2: Filter List of SNPs

• Download the perl script 23andMe_filter.pl
• There is one parameter that you need to enter:
• input = file containing 23andMe SNP file with SeattleSNP and GWAS Catalog SNPs (see here for more details)
• There is 5 optional parameters that you can enter:
• output = output file containing filtered SNP lists.  By default, _filter.txt is appended to the end of the input file
• OR = odds ratio cutoff (filter for scores greater than cutoff) [default = 2]
• PAM = PAM score cutoff (filter for scores less than cutoff) [default = 0]
• risk_status = status for GWAS Catalog risk allele,  Either "Homozygous", "Heterozygous" (which actually filters for both homozygous and heterozygous risk alleles), or "none" [default = "Heterozygous]
• allele_freq = set of parameters to describe allele frequency cutoff.  If provided, parameter must be the following format [genetic background]_[comparison type]_[threshold]  For example, European_gt_0.25. [default = "none?]
• Genetic background can be "European", "African", and "Asian"
• Comparison type can be "gt" for greater than or "lt" for less than
• Threshold corresponds to the population frequency.  Must be between 0 and 1.
• 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_filter.pl" and enter the required input parameter. See example below  (click to enlarge) .

• You can also enter in optional parameters (OR, PAM,  risk_status , and/or  allele_freq ).  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_ filter.pl" and enter the required input parameter. See example below  (click to enlarge).

• You can also enter in optional parameters (OR, PAM,  risk_status , and/or  allele_freq ).  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.