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 simulated annealing algorithms to perform these multipoint analyses. Simwalk2 was developed by Eric Sobel, Kenneth Lange, Daniel Weeks, Jeff O'Connell, and Goncalo Abecasis at UCLA.
Simwalk2 can be run on Helix or Biowulf.
Type simwalk2 on command line
This test run uses the files MAP.DAT, LOCUS.DAT, PEDIGREE.DAT and PEN.DAT from the Simwalk Example set, and the example sampling analysis (file BATCH-01.DAT) is being performed. These files can be copied from /usr/local/src/simwalk/SimWalk289/Examples.
% simwalk2 SimWalk2 version 2.91 Type of data analysis: Pedigree Sampling Locus data INPUT file: LOCUS.DAT Pedigree data INPUT file: PEDIGREE.DAT Map data INPUT file: MAP.DAT Individual OUTPUT files: MODEL-01.mmm Copy of all screen output: VIDEO-01.TXT Here 'mmm' is from the order within the input pedigree file, e.g., '001' for the first pedigree, etc. Working on data initialization ... WARNING. In the locus file: LOCUS.DAT for the following loci, minor adjustments had to be made to the allele frequencies to force them to sum to 1.0: CACNL1A1 pY2/1 KCNA5 S93 Map data file 'MAP.DAT' completed initialization; Locus data file 'LOCUS.DAT' completed initialization; Pedigree #001 completed initialization; All data completed initialization. Working on pedigree analysis ... Pedigree #001 ('20') working on simulated annealing ... (Found an initial consistent state.) 25% done ... 50% done ... 75% done ... Pedigree #001 ('20') completed simulated annealing. Pedigree #001 ('20') working on Markov chain Monte Carlo process ... 25% done ... 50% done ... 75% done ... Pedigree #001 ('20') completed Markov chain Monte Carlo process. Pedigree #001 ('20') completed all analyses. All individual pedigrees completed analysis. Please see the following output files. Individual OUTPUT files: MODEL-01.mmm Copy of all screen output: VIDEO-01.TXT Here 'mmm' is from the order within the input pedigree file, e.g., '001' for the first pedigree, etc. Program run completed!