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 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.

Version

Type simwalk2 on command line

Sample session

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!

Documentation

http://www.genetics.ucla.edu/software/simwalk_doc/