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MERLIN

MERLIN

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


Available

Version on CSC's Servers


Taito: 1.1.2


Usage

The program neds to be initialized before use.

On Taito use
module load biokit

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)

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

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

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

 


Discipline

Biosciences

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.


Support

servicedesk@csc.fi


Manual

More information about MERLIN can be found from the Merlin home page.