SAGE
Description
Statistical Analysis for Genetic Epidemiology (S.A.G.E.) is a collection of compiled C++ programs that perform a wide variety of genetic analyses. The range of functionality includes tools for:
- extracting summary statistics describing the data and evaluating general data quality
- estimating allele frequencies
- estimating heritability and familial correlations
- inferring mixture models for genetic transmission, and penetrance functions, including variable age of onset
- estimating identity-by-descent (IBD) allele sharing probabilities between relative pairs
- performing model-based linkage analysis
- performing model-free linkage analysis
- performing transmission/disequilibrium (TDT) analysis
- analyzing trait/allele associations
The programs of SAGE are intended to be used on the Helix platform of the Helix Systems. They are under /usr/local/sage/bin . To start the program, type the full path of the program followed by required parameters. SAGE programs include:
- assoc
- ageon
- decipher
- fcor
- freq
- genibd
- lodpal
- lodlink
- markerinfo
- mlod
- pedinfo
- reltest
- segreg
- sibpal
- tdtex
Version
Type /usr/local/sage/bin/pedinfo on command line
Sample session
Sage example files can be copied from /usr/local/sage/Examples.
Add to your path /usr/local/sage/bin if run sage programs a lot. This directory contains all executables in the package.% /usr/local/sage/bin/pedinfo InputFile.parameters InputFile.Pedigree PEDINFO -- 1 Aug 2006 14:04:05 -- [S.A.G.E. v5.1.1; 12 Dec 2005] COPYRIGHT (C) 2005 CASE WESTERN RESERVE UNIVERSITY Reading Parameter File....................done. Reading Pedigree File..................... from InputFile.parameters...........done. Sorting Pedigrees.........................done. Generating statistics.....................done. Analysis complete!For csh or tcsh users, issue this command: % set path=( /usr/local/eigensoft/bin ${path} )
For bash/ksh/sh users, issue this command: % PATH=/usr/local/eigensoft/bin:$PATH
Documentation
sage_UserDoc.pdf