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).

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