Chiamo

Record added by Jurg Ott (the original Rockefeller list)

0.2.1 (Oct 2007)

CHIAMO is a program for calling genotypes from the Affymetrix 500K Mapping chip. The program allows for multiple cohorts which have potentially different intensity characteristics that can lead to elevated false-positive rates in genome-wide studies. The underlying model has a hierarchical structure that allows for correlation between the parameters of each cohort. The output files produced by CHIAMO feed directly into both the programs SNPTEST and IMPUTE. CHIAMO was used to call genotypes for the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC).

Jonathan Marchini

http://www.stats.ox.ac.uk/~marchini/software/gwas/chiamo.html

Marchini, Spencer, Teo, Donnelly (2007), “A Bayesian hierarchical mixture model for genotype calling in a multi-cohort study”,