Description

MERLIN uses sparse trees to represent gene flow in pedigrees and performs rapid haplotyping, genotype error detection and affected pair linkage analyses (Abecasis et al, 2002).

Version

Type merlin on command line

Sample session

% merlin merlin.dat
MERLIN 1.1.2 - (c) 2000-2007 Goncalo Abecasis

References for this version of Merlin:

   Abecasis et al (2002) Nat Gen 30:97-101        [original citation]
   Fingerlin et al (2004) AJHG 74:432-43          [case selection for association studies]
   Abecasis and Wigginton (2005) AJHG 77:754-67   [ld modeling, parametric analyses]
   Fingerlin et al (2006) Gen Epidemiol 30:384-96 [sex-specific maps]
   Chen and Abecasis (2007) AJHG 81:913-26        [qtl association analysis, qtl simulation]


The following parameters are in effect:
                     Data File :      merlin.dat (-dname)
                 Pedigree File :      merlin.ped (-pname)
            Missing Value Code :         -99.999 (-xname)
                      Map File :      merlin.map (-mname)
            Allele Frequencies : ALL INDIVIDUALS (-f[a|e|f|m|file])
                   Random Seed :          123456 (-r9999)

Data Analysis Options
         General : --error, --information, --likelihood, --model [param.tbl]
      IBD States : --ibd, --kinship, --matrices, --extended, --select
     NPL Linkage : --npl, --pairs, --qtl, --deviates, --exp
      VC Linkage : --vc, --useCovariates, --ascertainment, --unlinked [0.00]
     Association : --infer, --assoc, --fastAssoc, --filter, --custom [cov.tbl]
     Haplotyping : --best, --sample, --all, --founders, --horizontal
   Recombination : --zero, --one, --two, --three, --singlepoint
       Positions : --steps, --maxStep, --minStep, --grid, --start, --stop
     LD Clusters : --clusters [], --distance, --rsq, --cfreq
          Limits : --bits [24], --megabytes, --minutes
     Performance : --trim, --noCoupleBits, --swap, --smallSwap
          Output : --quiet, --markerNames, --frequencies, --perFamily, --pdf,
                   --tabulate, --prefix [merlin]
      Simulation : --simulate, --reruns, --save, --trait []

Documentation

http://www.sph.umich.edu/csg/abecasis/Merlin/tour/
http://www.sph.umich.edu/csg/abecasis/Merlin/reference.html