- to compile pedsim:

g++ -O3 -o pedsim pedigree-simulator.cpp -mmacosx-version-min=10.5 

- download http://hapmap.ncbi.nlm.nih.gov/downloads/phasing/2009-02_phaseIII/HapMap3_r2/CEU/UNRELATED/

- gunzip

- edit hapmap_haps_and_recomb.pl for the path and chromosome loop

- see readme

grabbing all founders: ./hapmap_haps_and_recomb.pl 100 1000 sim-long.snps sim-long.haps sim-long.rec

- 100 1000 : see ./hapmap_haps_and_recomb.pl

- outbread: ./random_pedigree.pl 4 2 3 30 0.3 test.ped


- WF: ./random_wf_pedigree.pl 10 10 0.2 wf.ped

- to print: download http://www.graphviz.org/Download..php

then: ./pedtodot* sim.ped

- data:

./pedsim 0.0 1 0.0 0.0 0.0 sim-long.rec.1 sim-long.haps.1 test.ped test.long.ped test.long.dl test.long.ibd

interpret of test.long.ibd: first std pedigre, then codes for which founder chromosome

1 2 0 0 2 1  3 4  3 4  


See also

    Recombination in paternal haplotype of [family]:[indv] at locus 119 from 1 to 2

- holding out:

./hold_out_genotypes_snps.pl test.ped test.long.ped test.long.ped.hold

- disease example: 

./pedsim d 0.1 1.1 0.25 0.01 sim-long.rec.1 sim-long.haps.1 sim.out.ped with-disease with-disease-locus with-disease-ibd
