Version

2.91, installed in MURSKA

2.91, installed in HIPPU

Description

SimWalk2 is a computer application for haplotype, location score, identity by descent, and non-parametric statistical analyses on any size of pedigree. SimWalk2 performs these analyses using Markov chain Monte Carlo and simulated annealing algorithms.

SimWalk2 uses as input: the pedigree and locus data, a marker map, and, optionally, reduced penetrance values for a trait locus and other run-specifying parameters. SimWalk2 has been used successfully on data with over 1000 individuals per pedigree and over 30 markers per chromosome. The run time for SimWalk2 is linear in the number of individuals and the number of markers.

SimWalk2 is capable of many types of analyses.

• Haplotype analysis estimates the most likely set of fully typed maternal and paternal marker haplotypes at each individual in the pedigree.

• Location scores indicate the relative likelihood of several positions, among the marker loci, for the trait locus given the pedigree data and the marker map.

• Non-parametric analysis, also known as marker-allele sharing statistics or cluster analysis, is model-free and based on identity-by-descent (IBD).

• IBD analysis estimates the probabilities that pairs of individuals share marker alleles identical by descent, i.e., inherited from a common ancestor within the pedigree.

• The sampling option provides, for each input pedigree, a user-specified number of simulated pedigrees, each fully typed at all requested marker loci. The simulations do not alter the trait phenotypes, only the marker phenotypes.

• The setup option performs no likelihood-based analysis on the data. This option merely checks that the data files are consistent and that the pedigrees have no incompatibilities.

The above description was partially copied from http://www.well.ox.ac.uk/pub/genetics/simwalk2/DOCS/SimWalk2.txt

Usage

The program is installed on Murska (murska.csc.fi) and in Hippu (hippu.csc.fi).

The software needs to be initialized before use:

module load simwalk2

To run SimWalk2, type:

simwalk

In version 2.91, you need five input files:

• BATCH2.DAT a batch file (you must use the name BATCH2.DAT for this file typed with capital letters)

• a locus file

• a pedigree file

• a penetrance file

• a map file

You can convert LINKAGE file formats to MENDEL file formats using Mega2 program (installed in Hippu and Murska).

For interpretation of the output files, see the documentation below.

Documentation

References

Published research assisted by this software should always cite:

Sobel E and Lange K (1996) Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker sharing statistics Am J Hum Genet 58:1323-1337.

User support