Merlin

Pedigree file
Data file describing the pedigree file.
Genetic map file
Marker allele frequency file

Allele Sharing Linkage Analysis
Variance Component Linkage Analysis

Input Files

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

Pedigree file

1   1   0  0  1   1      x   3 3   x x
1   2   0  0  2   1      x   4 4   x x
1   3   0  0  1   1      x   1 2   x x
1   4   1  2  2   1      x   4 3   x x
1   5   3  4  2   2  1.234   1 3   2 2
1   6   3  4  1   2  4.321   2 4   2 2

Data file describing the pedigree file.

The first five columns are: family name, name, father, mother, gender.

A  some_disease
T  some_trait
M  some_marker
M  another_marker

Genetic map file

CHROMOSOME   MARKER          LOCATION
24           some_marker     123.4
24           another_marker  136.2

Marker allele frequency file

M some_marker
F 0.1 0.2 0.3 0.4
M another_marker
F 0.6 0.4

M some_microsatellite
A 152 0.5
A 154 0.4
A 156 0.1

Analysis

Allele Sharing Linkage Analysis

merlin -d merlin.dat -p merlin.ped -m merlin.map -f merlin.frq --npl

merlin -d merlin.dat -p merlin.ped -m merlin.map -f merlin.frq --pairs

Variance Component Linkage Analysis

merlin -d merlin.dat -p merlin.ped -m merlin.map -f merlin.frq --vc