Software / programs

hapLOH

hapLOH profiles and characterizes tumor genomes using data from SNP microarrays (Vattathil & Scheet, 2013). It is designed to be effective in difficult settings such as low tumor purity, subclones or detecting clonal mosaicism in normal tissue. For details on use and further documentation please visit our Google Sites page.

The software (written by Selina Vattathil and Jerry Fowler) is freely available under The MIT License at http://haploh.scheetlabsoftware.org. For additional inquiries, please contact Selina Vattathil (svattathil@utexas.edu).

hapLOHseq

hapLOHseq has been developed for the detection of subtle allelic imbalance events from next-generation sequencing data. hapLOHseq is a sequencing-based extension of hapLOH, which is a method for the detection of subtle allelic imbalance events from SNP array data. hapLOHseq is capable of identifying events of 10 mega-bases or greater occurring in as little as 16% of the sample using exome sequencing data (at 80x) and 4% using whole genome se-quencing data (at 30x), exceeding the capabilities of existing software. hapLOHseq runs on Linux and MacOSX platforms. For details on use and further documentation please visit our Google Sites page.

The software (written by Anthony San Lucas) is freely available under The MIT License for Linux (http://scheet.org/software/haplohseq_linux-0.1.2.tar.gz) and Mac OS X (http://scheet.org/software/haplohseq_macosx-0.1.2.tar.gz) bundles. For additional inquiries, please contact Anthony San Lucas (fasaan@mdanderson.org).

CiDD

Cancer in silico Drug Discovery (CIDD) is a platform to integrate data from the TCGA, Connectivity Map (CMap) and Cancer Cell Line Encyclopedia to facilitate and automate discovery of candidate drug compounds with the ultimate goal for treatment or chemo-prevention of cancer. Our manuscript is currently under review. CiDD may be obtained by visiting cidd.scheetlabsoftware.org.

vtools

vtools is a set of tools for annotating and tracking sequence variation for large-scale exome sequencing projects (San Lucas et al, 2011). It was developed and authored by Anthony San Lucas and Bo Peng, and is available for download at varianttools.sourceforge.net.

YETI

phylogenY-aware Effect size Tests for Interaction (YETI) is a statistical framework for detecting genetic interactions. This is joint work with Dr. Yong Chen and Yulun Liu. R code for YETI can be accessed here and also/eventually at Yong Chen's site.

Haploscope

Haploscope is a tool for visualizing haplotype diversity, based on a cluster-based model for haplotype variation (Scheet & Stephens, 2006). It automates the production of images such as those in Jakobsson et. al. (2008). It is written in Java (by Anthony San Lucas) and may be obtained by visiting haploscope.scheetlabsoftware.org.

Haploscope is freely downloadable with a GNU GPL v3 license.

fastPHASE

fastPHASE is a program to estimate missing genotypes and unobserved haplotypes. It is an implementation of the model described in Scheet & Stephens (2006). This is a cluster-based model for haplotype variation, and gains its utility from implicitly modeling the genealogy of chromosomes in a random sample from a population as a tree but summarizing all haplotype variation in the "tips" of the trees.

The program offers additional functionality, as well, including the following: estimation and correction of genotyping errors based on patterns of linkage disequilibrium (Scheet & Stephens, 2008), haplotype-based association mapping of binary phenotypes, estimation of missing genotypes from low-coverage sequencing data. We are in the process of developing a web-based tutorial for fastPHASE and will be updating this space soon.

fastPHASE is available as a Mac OS and a Linux executable. Documentation is available here.