PBAT: a comprehensive software package for genome-wide association analysis of complex family-based studies

Hum Genomics. 2005 Mar;2(1):67-9. doi: 10.1186/1479-7364-2-1-67.


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.

MeSH terms

  • Family
  • Genome, Human*
  • Genomics / instrumentation
  • Genomics / methods*
  • Humans
  • Models, Genetic
  • Polymorphism, Single Nucleotide
  • Software*