Simwalk2
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Simwalk2
General description
SimWalk2 is a statistical genetics computer application for haplotype, parametric linkage, non-parametric linkage (NPL), identity by descent (IBD) and mistyping analyses on any size of pedigree. SimWalk2 uses Markov chain Monte Carlo (MCMC) and simulates annealing algorithms to perform these multipoint analyses.
The source code of Simwalk2 can be downloaded and compiled for most architectures.
Application homepage
http://www.genetics.ucla.edu/software/simwalk_doc/
Proper citation
- Sobel E and Lange K (1996) Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker sharing statistics. American Journal of Human Genetics 58:1323-1337.
- Sobel E, Sengul H, Weeks DE (2001) Multipoint estimation of identity-by-descent probabilities at arbitrary positions among marker loci on general pedigrees. Human Heredity 52:121-131.
- Sobel E, Papp JC, Lange K (2002) Detection and integration of genotyping errors in statistical genetics. American Journal of Human Genetics 70:496-508.
Quick start
To start running simwalk2 you need to construct the five input-files that simwalk requires (map, locus, pedigree, penetrance and batch file). As an input example you may download MAP.DAT, LOCUS.DAT, PEDIGREE.DAT, PEN.DAT and BATCH.DAT.
Input file formats
There are five different files in Simwalk2, which each has its own file format. An extensive introduction to these file formats can be found on the program's homepage.
Output files
There is a number of output files that are produced, depending on the type of analysis run. More info on the different file formats can be found on the Simwalk2 homepage. Common for all runs are the VIDEO-**.TXT and ERROR-**.TXT, displaying the output and error messages from the program respectively.