AutoSNPa

About this program

This program is designed to aid the identification of regions of Identity By Descent (IBD) in consanguineous individuals by visually presenting the SNP genotype data ordered by physical or genetic distances.

The program uses the text files (with a *.xls file extension) created by Affymetrix, however it may be a relatively simple process to upgrade the program to use data from other sources.

Initially the program was written for the 10K SNP datasets, but with the advent of the 250k NSP and STY SNP data files, the program was completely rewritten to speed up the presentation of the data and to create smaller output files. The new version no longer creates Excel files; instead it creates a colour coded web page.

AutoSNPa versus IBDFinder

This program is designed to work with individuals from the same family or where they are expected to have the same haplotype around the disease loci. Consequently it reduces the number of false positives that may occur with IBDFinder, but does require suitable pedigrees that can be difficult to find.

This program and its instruction file is currently hosted on mirror of my old department web site and can obtained from here. A copy of the user guide is also kept on this site here.

This program has been published in Human mutation

Citation

Carr IM, Flintoff K, Taylor GR, Markham AF & Bonthron DT (2006). Interactive visual analysis of SNP data for rapid autozygosity mapping in consanguineous families. Human Mutation, 27:1041-6

Computer requirements

This program runs on Microsoft Windows, using the .NET 2.0 environment which can be obtained from here.