AIP software: genosim
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ANIMAL IMPROVEMENT
PROGRAM

genosim Simulate genotypes, breeding values, and phenotypes; simulate DNA sequence read depth (numbers of A and B alleles); and resolve SNP conflicts between parent and offspring genotypes

Downloads Version 4 program, example files, and executable

Programs pedsim.f90
markersim.f90
genosim.f90
geno2seq.f90
phenosim.f90
conflict.f90
Extremely simple pedigree program (usually not used because real pedigree is used; see details below)

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
offset2Can have the same value as offset1 or different to pick different markers
depth1Sequence read depth; if simulating chip data, set the value to 35
error1Error rate for chip or sequence data (extremely low for chip data)
chromosome.data Check after running markersim to be sure that the marker pattern is as intended
*.optionsProvides 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.

References 2014  VanRaden, P.M., and C. Sun. Fast imputation using medium- or low-coverage sequence data. Proc. 10th World Congr. Genet. Appl. Livest. Prod., Vancouver, Canada, Aug. 17–22, Comm. 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.

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)

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@ars.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
 National Association of Animal Breeders



Last Modified: 01/12/2017