Version

2.51 (FastSLINK), installed in HIPPU

Description

In a linkage study it is important to know if the pedigrees you have collected (or plan to collect) will be sufficient to detect linkage. The power to detect linkage depends on a variety of factors, such as the structure of the pedigree, the number of affected individuals, and the informativeness of the markers. The SLINK program allows one to carry out such power calculations by simulating genotypes at one locus given the phenotypes at another locus linked with the first locus. If one is interested in simulating under no linkage (eg. to investigate exclusion possibilities or p-values), the SLINK program may also be used but other programs such as SIMULATE are in that case much more efficient than SLINK.

SLINK is based on the LINKAGE programs version 4.9 (Lathrop et al., 1984) and accepts slightly modified LINKAGE data files. The simulated pedigrees may be analyzed by either the standard LINKAGE programs or by the special companion programs (MSIM, ISIM, or LSIM), which have been modified to read one replicate of the pedigrees at a time, rather than reading in the entire pedigree file. In addition, the companion programs provide some simple statistical summaries.

Usage

Programs are installed in HIPPU (hippu.csc.fi).

To add slink and related programs to you path in HIPPU, type:

module load slink

Running the simulations requires the following steps:

1. slink (to create the pedigree data)

2. unknown (to create files for msim, isim and lsim)

3. msim, isim, or lsim (linkage analysis programs)

Slink requires three input files:

1. slinkin.dat: a special parameter file

2. simdata.dat: a standard LINKAGE data file in MLINK-format

3. simped.dat: a standard LINKAGE pedigree file with an additional column inserted after the last phenotype column. This additional column in the SLINK pedigree file 'simped.dat' contains the availability code, which controls what type of phenotypes are written to the output file. These codes are consistent with the codes used by the simulation program SIMLINK (Boehnke, 1986; Ploughman and Boehnke, 1989).

There are some parameters that need to be set when compiling and can not be changed by the user (please see program documentation for details). The default parameters are listed when the programs start . If you need to set these parameters, please contact CSC user support.

Documentation

The Slink documentation explains the file formats and how to perform the simulations. The Figure 1 in the documentation is very useful.  A HTML version of the manual is available from the University of Pittsburgh.

References

Please use the following two references when reporting results based on slink:

Ott J (1989) Computer-simulation methods in human linkage analysis. Proc Natl Acad Sci USA 86:4175-4178

Weeks DE, Ott J, Lathrop GM (1990) SLINK: a general simula- tion program for linkage analysis. Am J Hum Genet 47:A204 (abstr)

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