Solar on Helix
SOLAR is a package of software to perform several kinds of statistical genetic analysis, including linkage analysis, quantitative genetic analysis, and covariate screening. The name SOLAR stands for "Sequential Oligogenic Linkage Analysis Routines."
Solar was developed by researchers at the Southwest Foundation for Biomedical Research.
New Solar users should send email to staff@helix.nih.gov asking to be registered as a Solar user. The Solar package requires each user to be registered.
If you expect to run more than one or two Solar jobs, please use Solar on Biowulf
Running a Solar job
Once you have been registered as a Solar user, you can run Solar by typing 'solar' at the Helix prompt.Sample session (user input in bold):
helix% solar
SOLAR version 4.1.0 (Official), last updated on June 07, 2007
Copyright (c) 1995-2007 Southwest Foundation for Biomedical Research
Enter help for help, exit to exit, doc to browse documentation.
solar> load pedigree plains_ped.txt
Unloading current pedigree data ...
Unloading current marker data ...
Loading pedigree data from the file plains_ped.txt ...
solar> load marker plainschr16_mrk.txt
Getting initial estimates of allele freqs from the marker data ...
Loading marker data from the file plainschr16_mrk.txt ...
solar> verbosity min
solar> freq mle
Running allfreq for marker rs8466 ... iter 9 delta loglike = 0.5072
Running allfreq for marker rs763053 ... iter 7 delta loglike = 0.1612
[...]
solar> load map plainschr16_map.txt
solar> mibd prep loki
Preparing input files for Loki multipoint IBD computation ...
The following files have been created:
lkmibd.data - pedigree/genotype data
lkmibd.prep - prep parameter file
lkmibd.loki - loki parameter file
mibdchr16.loc - map file for SOLAR plots
Move the file mibdchr16.loc to the directory where the Loki-computed IBDs
will be stored.
solar> quit
helix%
Documentation
Solar documentation at the SFBR website.
