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**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 genotypesDownloads
Version 4 program, example files, and executablePrograms
pedsim.f90
Extremely simple pedigree program *(usually not used because real pedigree is used; see details below)*markersim.f90genosim.f90geno2seq.f90phenosim.f90conflict.f90Program order
Simulate genotypes from SNP chips
pedsim.f90 *(optional)* → markersim.f90 → genosim.f90 → conflict.f90Simulate DNA sequence read depths
pedsim.f90 *(optional)* → markersim.f90 → genosim.f90 → geno2seq.f90Simulate 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.f90Convert chip genotype data and simulate sequence format
geno2seq.f90Check parentage conflicts, count conflicts by animal and chip, correct Mendelian errors, and fill missing SNPs using parental genotypes where possible
conflict.f90Program files
Input/output files
Listed at beginning of source code file for each programchips.txt
Used by markersim.f90 and geno2seq.f90; parameter definitions:chip
Sequential number for each chipreduce1
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 beginningreduce2
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 usedoffset2
Can have the same value as offset1 or different to pick different markersdepth1
Sequence read depth; if simulating chip data, set the value to 35error1
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 definitionspedsim.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 ancestorsgenotype.data0
Indicates which individuals are genotyped with which chipphenotype.data0
Indicates reliability of conventional estimated breeding value (**EBV**) and parent average (**PA**) in truncated dataphenotype.later0
Indicates reliability of conventional EBV and PA in final dataOutput 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 LaboratoryAgricultural Research Service, USDA **Chuanyu Sun**Biostatistics and BioinformaticsNeogen Corporation


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