genosim	Simulates genotypes, breeding values, and phenotypes; simulate sDNA sequence read depth (numbers of A and B alleles); and resolves SNP conflicts between parent and offspring genotypes
Downloads	Version 4 program, example files, and executable
Programs	pedsim.f90	Extremely simple pedigree program (usually not used because real pedigree is used; see details below)
	markersim.f90
	genosim.f90
	geno2seq.f90
	phenosim.f90
	conflict.f90
Program order	Simulate genotypes from SNP chips	pedsim.f90 (optional) → markersim.f90 → genosim.f90 → conflict.f90
	Simulate DNA sequence read depths	pedsim.f90 (optional) → markersim.f90 → genosim.f90 → geno2seq.f90
	Simulate phenotypes from either SNP genotypes or simulated DNA sequence	pedsim.f90 (optional) → markersim.f90 → genosim.f90 → conflict.f90 (optional for simulated DNA sequence) → findhap.f90 → phenosim.f90
	Convert chip genotype data and simulate sequence format	geno2seq.f90
	Check parentage conflicts, count conflicts by animal and chip, correct Mendelian errors, and fill missing SNPs using parental genotypes where possible	conflict.f90
Program files	Input/output files	Listed at beginning of source code file for each program
	chips.txt	Used by markersim.f90 and geno2seq.f90; parameter definitions:
		chip	Sequential number for each chip
		reduce1	1 = Contains all simulated markers 2 = Contains every other simulated marker 3 = Contains every 3rd marker … etc.
		offset1	Number of markers to shift from the beginning
		reduce2	Can have the same value as reduce1, but if the value is different from that used for reduce1, all the markers picked by reduce1 and reduce2 will be used
		offset2	Can have the same value as offset1 or different to pick different markers
		depth1	Sequence read depth; if simulating chip data, set the value to 35
		error1	Error rate for chip or sequence data (extremely low for chip data)
	chomosome.data	Check after running markersim to be sure that the marker pattern is as intended
	*.options	Provides detailed parameter definitions
pedsim.f90 details	Input	pedsim.options (please read this file for detailed explanations of each parameters)
	Output	pedigree.file	Supplies pedigrees and birth dates (or years) of genotyped animals plus ancestors
		genotype.data0	Indicates which individuals are genotyped with which chip
		phenotype.data0	Indicates reliability of conventional estimated breeding value (EBV) and parent average (PA) in truncated data
		phenotype.later0	Indicates reliability of conventional EBV and PA in final data
		Output files can be easily created based on real pedigree, and the format is same as the files in the Example_Output folder. If phenotypes are not simulated, only the first 2 files need to be created base on real pedigree.
Version differences	4 vs. 3	Added geno2seq.f90 to generate DNA sequence read depth (released August 2014)
	3 vs. 2	Allowed definition of multiple chips (used 2012–13, but not released)
	2 vs. 1	Generated linkage disequilibrium in base population (used 2010–11, but not released)
	1	Assumed no linkage disequilibrium in base population (used 2007–09, but not released)
References	2015	VanRaden, P.M., C. Sun, and J.R. O'Connell. Fast imputation using medium- or low-coverage sequence data. BMC Genet. 16:82.
	2014	VanRaden, P.M., and C. Sun. Fast imputation using medium- or low-coverage sequence data. Proc. 10th World Congr. Genet. Appl. Livest. Prod., 179.
	2013	VanRaden, P.M., D.J. Null, M. Sargolzaei, G.R. Wiggans, M.E. Tooker, J.B. Cole, T.S. Sonstegard, E.E. Connor, M. Winters, J.B.C.H.M. van Kaam, A. Valenti, B.J. Van Doormaal, M.A. Faust, and G.A. Doak. Genomic imputation and evaluation using high-density Holstein genotypes. J. Dairy Sci. 96:668–678.
	2011	VanRaden, P.M., J.R. O'Connell, G.R. Wiggans, and K.A. Weigel. Genomic evaluations with many more genotypes. Genet. Sel. Evol. 43:10.
	2008	VanRaden, P.M. Efficient methods to compute genomic predictions. J. Dairy Sci. 91:4414–4423.
License	Fortran package genosim is public domain and was developed with U.S. taxpayer funding. Accurate results are not guaranteed. Please report any bugs to paul.vanraden@usda.gov. You may modify, improve, use, and redistribute the code to anyone for any purpose. Or, you can ask Paul to make changes that could benefit U.S. evaluations and other users.

 Paul VanRaden
 Animal Genomics and Improvement Laboratory
 Agricultural Research Service, USDA

 Chuanyu Sun
 Biostatistics and Bioinformatics
 Neogen Corporation