Bioinformatics Applications UNPHASED - Association and TDT for haplotypes

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UNPHASED is a suite of programs for association analysis of multilocus haplotypes from unphased genotype data. UNPHASED currently includes the following programs:

• TDTPHASE: TDT and HHRR analysis for case-parent trios
• COCAPHASE: case/control data
• QTPHASE: quantitative trait in unrelateds
• PDTPHASE: pedigree disequilibrium test
• QPDTPHASE: quantitative trait PDT

The programs extend previous methods to include haplotypes and missing genotypes. The TDTPHASE program uses the ETDT method for phase-certain haplotypes and the HHRR method for uncertain haplotypes. The COCAPHASE program uses the same method as EHPLUS. In addition, both programs include conditional tests that allow for linkage disequilibrium with previously associated loci. Tests of individual haplotypes are possible as are pairwise and wildcard comparisons of haplotype risks. The programs can also calculate D' and r^2 measures of LD. Chromosome X data is allowed.

A graphical interface is available through GLUE. On unix systems displaying X-windows, unphased.sh is a script which starts a native graphical interface.

Detailed description of unphased