[Version 11/13/05+] Specify this file at “Analysis/Open group/Other information/SNP information file”. The SNP information comes from Affymetrix annotation CSV files. The fragment length information is used for filtering SNPs.

The allele frequency of an ethnic group (Asian, African American or Caucasian) can be specified at “Tools/Options/Chromosome/Allele A frequency” and used in linkage analysis or allele sharing analysis. In version 5/18/06+, the allele frequency can be specified as "Compute from data" here so the arrays used in the array list file will be used to compute allele A frequency.

When an allele frequency is 100% or 0% in the genome information file, it will be truncated to 0.001 or 0.999 before using them in linkage analysis. Non-specified allele frequency will be used as 50% for both A and B allele.

Download SNP information files

Unzip and use these files: Mapping 10K 2.0, Mapping 100K, Mapping500K, SNP 6.0

Make SNP information file

This Python program can be used or modified to make dChip genome information files from recent Affy annotation CSV files of SNP arrays such as "GenomeWideSNP_6.na24.annot.csv". Download and install Python, start Python GUI, use "File/Open" to open "snp6_snp_info.py" (in the same directory as CSV and PSI files), modify file names in the program if necessary, and select "Run/Run Module".