Sciences and methods > Biosciences > Programs > MERLIN
 
Sisältö
 
Tehdyt toimenpiteet

MERLIN

Version

1.1.2 installed in Hippu

1.1.2 installed in Murska

1.1.2 installed in Vuori

Description

MERLIN is a very fast linkage analysis package that uses efficient data structures (sparse trees) to represent the traversal of genes in pedigrees.

MERLIN can be used for:

  1. non-parametric multipoint linkage analysis

  2. variance component analysis

  3. IBD (identical by descent) and kinship estimation

  4. haplotype reconstruction

  5. detection of genotyping errors

  6. allele dropping simulations

Usage

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

The software needs to be initialized before use:

module load merlin

MERLIN requires the following input files:

  1. Pedigree file in a standard LINKAGE format

  2. Map file

  3. Locus file (can be replaced by a LINKAGE format locus file)

  4. Allele frequency file (optional)

Take a look at a commented example of the input data files.

To run MERLIN, type merlin followed by command line options:

merlin -d linkage.loci -p linkage.pre -m linkage.map --npl --trim --bits 30

Some of the most widely used command line options are:

-d filename the name of locus file
-p filename the name of the pedigree file
-m filename the name of the map file
-f filename the name of the frequency file.
--error turn error detection on
--npl perform nonparametric linkage analysis.
--vc perform variance component analysis.
--steps:n Carry out analyses at n steps between each pair of markers.
--best output the best haplotype configuration
--singlepoint perform analysis in two point (disease vs. marker) mode
--simulate perform allele dropping simulation. In this mode, the founders are assigned random alleles from the allele frequency distribution. The propagation of alleles is then simulated, and missing data is introduced to the same loci as in the original data. Finally, the simulated data set is analyzed as the original would be.
--trim drop noninformative individuals from the analysis
--bits:n Sets the maximum number of bist per pedigree. The number of bits corresponds to 2n-f, where n equals to the number of individuals and f the number of founders in the pedigree.

A full description of Merlin command line parameters can be viewed at Merlin reference sheet in the University of Michigan.

Documentation

A more detailed description about how to run MERLIN is available at MERLIN home page in the University of Michigan.

References

When you use Merlin, cite:

Abecasis GR, Cherny SS, Cookson WO and Cardon LR, Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet (2002) 30: 97-101.

User support

Saren Ari-Matti +358 9 457 2282 Ari-Matti.Saren at csc.fi