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== Input files ==
== Input files ==
* A ped file, with 5 colums [[http://www.sph.umich.edu/csg/abecasis/merlin/tour/ see merlin documentation]]. An example ped file is as follows
* A ped file, with 5 colums [[http://www.sph.umich.edu/csg/abecasis/merlin/tour/ see merlin documentation]]. An example ped file is as follows (Note that you can mix trios with other nuclear families in the same VCF file):
quartet1 p1 0 0 1
quartet1 p1 0 0 1
quartet1 p2 0 0 2
quartet1 p2 0 0 2
quartet1 p3 p1 p2 1
quartet1 p3 p1 p2 1
quartet1 p4 p1 p2 1
nuc1 p5 0 0 1
nuc1 p6 0 0 2
nuc1 p7 p1 p2 1
nuc1 p8 p1 p2 1
nuc1 p9 p1 p2 1
trio1 p10 0 0 1
trio1 p11 0 0 2
troi1 p12 p1 p2 1
trio2 p13 0 0 1
trio2 p14 0 0 2
troi2 p15 p1 p2 1
* A VCF file [[http://www.1000genomes.org/node/101 VCF specs]]. It can contain variant information for more individuals than in the ped file.
* A VCF file [[http://www.1000genomes.org/node/101 VCF specs]]. It can contain variant information for more individuals than in the ped file.
