Software Developed at Vanderbilt CHGR

LD-PLUS: When presenting statistics from a candidate gene study, or a region of interest from a genome-wide association study, it is useful to see various SNP-wise values in the context of linkage disequilibrium patterns.  LD-Plus presents a familiar Haplo-view style correlation plot that is annotated with haplotypes, haplotype blocks, and haplotype frequencies, along with continuous and categorical SNP statistics.  

WASP: Whole-genome Association Study Pipeline (WASP) was designed to aid in retrieving, evaluating, formatting, and analyzing genotypic and clinical data from the latest large-scale genotyping studies. WASP implements a battery of quality control procedures to assess the data. Among the currently available procedures are the examination of marker and sample genotyping efficiency, allele frequency calculations, checks of Mendelian error (if applicable) and gender discrepancies (based on available chromosome X and Y genotypes), and tests of Hardy-Weinberg Equilibrium.

MDR: Software to examine multi-locus genotype patterns associated with susceptibility to complex multifactorial diseases. Designed and implemented by Lance W. Hahn, Marylyn D. Ritchie, and Jason H. Moore.

PowerTrim: An Automated Decision Support Algorithm for Preprocessing Family-Based Genetic Data. American Journal of Human Genetics. 71 (Suppl): 570, 2002. Thornton TA, Haines JL.

PMD:   Software to discover perfect and near-perfect associations between a phenotype and 1 and 2-SNP genotypes embedded in large (100,000+ SNPs) genome-wide data. Currently under review. Lance W. Hahn and Marylyn D. Ritchie.

GIST:  A method for detecting association between marker genotypes and IBD sharing at the same locus.  Such an association will indicate that the marker itself, or one in linkage disequilibrium with it, could account for the observed linkage signal (at least partially).  The software can be used to analyze affected sibship data.