Commercially available products mainly differ in the coverage to price ratio, which rapidly changes with the development and release of new panels. In the GWA procedure section of this protocol (see Box 2) we will go through how to calculate the coverage of available genotyping panels for the markers genotyped in the HapMap project. The script that will be used for calculating the coverage implements the algorithm published by Barrett and Cardon 17. A new release of the HapMap project with a more complete selection of SNPs genotyped for a larger number of individuals is likely to be released in the near future as well as new commercially available genotyping panels. The coverage calculations can easily be repeated for additional panels by running the script provided, using updated reference data and new SNP lists. Guidelines on how to quality-check and analyse generated GWA and candidate gene data will be presented in subsequent Nature Protocols.
