Software

Various freely-available tools developed by our group

PLINK

A toolset for single nucleotide polymorphism (SNP) and copy number variant (CNV) whole-genome association studies. Includes functions for data management, QC, summary statistics, association analysis and IBD/ancestry inference (Purcell et al., 2007).

PLINK/SEQ

Designed for the analysis of variation data from next-generation sequencing studies (VCF-oriented), primarily exome sequencing studies.

GPC: Genetic Power Calculator

Web service for basic power calculations for case/control and quantitative trait family-based and population-based association studies, and for QTL linkage studies (Purcell et al., 2003 and Sham et al., 2000).

XHMM

Designed to detect copy number variants (CNV) in targetted sequencing studies by an analysis of read depth data (Fromer et al., 2012).

INRICH

Software for gene-set enrichment analysis for GWAS, CNV and other genome-wide study designs, based on a genomic, interval-based permutation scheme (Lee et al., 2012).

Genebook

Genebook is designed to create simple web-based databases that provide results from genetic studies. Think of a genebook as an interactive version of a supplementary table in a typical journal article.

 

Redundant, unsupported software and scripts

These are provided primarily for historical reasons.

  • famtypes A small utility for sanity-checking and summarizing pedigree files
  • whap A tool for haplotype analysis. whap is a C/C++ program for haplotype analysis. It can handle SNPs or multiallelic markers; disease or quantitative traits; unrelated individuals or family-based samples. In particular, it is possible to test nested models in a flexible manner that enables various types of conditional analysis (e.g. whether a particular haplotype can explain all the association signal at a locus, or whether a particular variant has any effects independent of the effects of correlated haplotypes). An example application of whap is described in Curran et al. (2005).
  • L-POP Latent class analysis model for detecting population stratification. L-POP is a C/C++ program to detect population stratification in samples of unrelated individuals. It uses an approach similar in spirit to that used in STRUCTURE, except it is based on latent class analysis. The method has been described in Purcell & Sham (2004).
  • MODEL: Online tool (currently not operational) for genetic association analysis. This tool provides a simple interface from which case/control and TDT analyses can be conducted, for the analysis of one or more samples simultaneously. A number of genetic models can be compared (e.g. multiplicative, dominant, etc); genotypic relative risks and/or population allele frequencies can be equated across samples or tested for heterogeneity.

Behavior genetics and twin analysis

  • BGIM: An introductory online tutorial to twin analysis, this site provides a collection of modules I created in 2001, designed to offer a gentle introduction to some of the fundamental quantitative genetic concepts in twin studies. In addition, some simple descriptions of other statistical genetic concepts such as linkage disequilibrium and maximum likelihood estimation can be found by following this the above link.
  • G x E in twin analysis: Mx scripts for continuous moderator models This link provides a collection of Mx (a freely available model-fitting package developed by Mike Neale, that is commonly used for modeling genetically-informative family data) scripts that accompany Purcell (2001)
  • DeFries-Fulker twin analysis: Mx scripts for DF analysis in proband-selected twin samples. This link provides a collection of Mx scripts that accompany Purcell & Sham (2003)

© Purcell Lab 2012-2015