Affymetrix GenomeWide6

Affymetrix’s software packages (e.g. Genotyping Console) provide a method to export the genotypes of every sample within a study to a text file. The files are also known as CHP export files because of the raw files they stem from.
You must provide one genotype file per sample (do not use the option of all samples in a single file). You may find the procedure to follow in the documentation of your Affymetrix software. (Affymetrix Genotyping Console Manual)

GWASpi will load the genotypes from these files. You mustĀ  store allĀ  genotype files to be loaded within a single folder (do not add any other files under that directory, only genotype files!). GWASpi will scan that directory for every file in it and start loading them.
You will also need to provide Affymetrix’s Annotation file for your array, which can be downloaded from their site. Do not alter the name of this file, as GWASpi needs it for ascertaining the version of your annotation data.

Sample information may be left aside at this stage, so that dummy samples will be created in the database, allthough it is recommended to provide sample information in a separate file as explained in Sample Info & Phenotype file.

Note: The Sample IDs will be read in GWASpi based on the filename as follows: Affymetrix prepends the Sample ID you introduced in the Genotyping Console (in the following example 10034) to the CHP export file name, optionally followed by the technology (_GW6) and the algorithm used for the calling (.birdseed-v2), and finally the extension (.txt or .chp)
CHP export file name: 10034_GW6.birdseed-v2.txt

Example of an Affymetrix Genowide 6.0 exported genotype file:
#CHP File=E:\GWS_data\AffyGW6\Call\10034_GWS6.birdseed-v2.chp
#Exec GUID=0000022872-1242577917-XXXXXXXXXXXXXXXX
SNPID Call Confidence Forced Call Signal A Signal B
SNP_A-2131660 AB 0.008552666 AB 2277.995 2602.922
SNP_A-1967418 BB 0.02126426 BB 243.9881 1013.824
SNP_A-1969580 BB 0.001222849 BB 1387.224 4458.214
SNP_A-4263484 AB 0.008405269 AB 1949.549 1341.844
SNP_A-1978185 AA 0.004376289 AA 846.2842 265.1265
SNP_A-4264431 AB 0.001437925 AB 1529.916 1118.775
SNP_A-1980898 AB 0.003524371 AB 855.9641 669.3145