This page serves as an index for the applications written and distributed by the Yandell, Marth, and Quinlan labs. Each item may include links to: documentation, code, and publications.
Software is listed with most recent releases first.
A software package that identifies genes with a statistical excess of damaging de novo mutations among individuals with a genetic disease. VARPRISM incorporates functional variant prediction information (the VAAST CASM score) to improve the statistical power of risk gene mapping and controls for local mutation rate heterogeneity. The beta version of VARPRISM is currently available for download.
Variant Annotation,Variant Calling
An open-source genome analysis platform that accomplishes alignment, variant detection and functional annotation of a 50× human genome in 13 h on a low-cost server and alleviates a bioinformatics bottleneck that typically demands weeks of computation with extensive hands-on expert involvement.
A disease-gene identification tool designed for high-throughput sequence data in pedigrees.
Phenotype Tools,Variant Prioritization
Integrates phenotype, gene function, and disease information with personal genomic data for improved power to identify disease-causing alleles.
Probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences.
A Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
Provides an informatics infrastructure for a laboratory, department, or research institute engaged in the large-scale analysis of genomes and their annotations.