Table 1

Summary of various components of UPDG.

UPDG component


Combines genotype and intensity data of individual DNA GWAS from separate files

Estimates allele frequencies of markers from DNA pools and performs adjustment correcting for allelic preferential amplification with the methods based on Hoogendoorn et al. (2000), Meaburn et al. (2006) and Craig et al. (2005), and generates input data files for the subsequent step of nested ANOVA

Removes SNPs with minor allele frequencies and call rates below a user-specified threshold and generates filtered input data file for nested ANOVA


Carries out nested ANOVA in R environment

Organizes results from nested ANOVA and generates a summary of markers with p values below a user-specified threshold

Generates summary information on estimated allele frequencies for markers

Ho et al. BMC Genetics 2012 13:1   doi:10.1186/1471-2156-13-1

Open Data