PBAT: a comprehensive software package for genome-wide association analysis of complex family-based studies.
The PBAT software package (v2.5) provides a unique set of tools for complex family-based association analysis at a genome-wide level. PBAT can handle nuclear families with missing parental genotypes, extended pedigrees with missing genotypic information, analysis of single nucleotide polymorphisms (SNPs), haplotype analysis, quantitative traits, multivariate/longitudinal data and time to onset phenotypes. The data analysis can be adjusted for covariates and gene/environment interactions. Haplotype-based features include sliding windows and the reconstruction of the haplotypes of the probands. PBAT's screening tools allow the user successfully to handle the multiple comparisons problem at a genome-wide level, even for 100,000 SNPs and more. Moreover, PBAT is computationally fast. A genome scan of 300,000 SNPs in 2,000 trios takes 4 central processing unit (CPU)-days. PBAT is available for Linux, Sun Solaris and Windows XP.
Van Steen
Kristel
K
Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
Lange
Christoph
C
D005190:Family; D015894:Genome, Human; D023281:Genomics / Q000295:instrumentation / Q000379:methods*; D006801:Humans; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D012984:Software