View Full Version : GenoChip conversion utility

Ann Turner
12-02-2012, 04:44 PM
I have written a spreadsheet macro to convert the GenoChip raw data download to the format used by 23andMe, which many 3rd party utilities can handle. It covers only data lines with rs numbers (chromosomes 1-22 and X). James Lick is covering mtDNA SNPs, and Y SNPs will also need special handling.

I have only one test case to validate the output file, so this is definitely a beta version :)

There was very good concordance between the GenoChip and corresponding SNPs in the volunteer's 23andMe raw data download. David Pike's utility http://www.math.mun.ca/~dapike/FF23utils/diffs.php reported

"0.021 % (22) of the 102789 SNP results differ"

Nine of those may actually be differences in plus/minus orientation (e.g. GG in one file and CC in the other).

Please write to me directly [email protected] if you'd like a copy of the spreadsheet GenoConvertTemplate.xlsm. In return, I will ask for your feedback on the instructions, general method, any refinements, and how the output file fares when used with your favorite 3rd party utilities. Note that the output file uses Build 37 numbers for the chromosomal locations of the SNPs. FTDNA currently uses Build 36 numbers, so you may not be able to mix and match files in utilities that key off the SNP position, such as David Pike's utility above.

You are welcome to post feedback here.