SimuQTReal - gc5k/GEAR GitHub Wiki
###Simulation for quantitative traits using binary genotype data###
Subcommand: simuqt-real
Options
--bfile
Specify the binary genotype file.
--poly-effect
It generates polygenic effects from the standard normal distribution. By default, it is polygenic model for the simulated data.
--effect
Specify the universal effect for each loci. It defaults to 0.5.
--poly-effect-sort
It generates polygenic effects from the standard normal distribution. Different from --poly-effect, this option will sort the genetic effects in ascending order, so that the first marker has the smallest effect and the last the biggest.
--effect-file
Specify the file that has the effect for each locus, one element per line.
--refallele-effect-file
Specify the SNP name, reference allele, and effect in the file. Each line has three items: SNP name, reference allele, and the effect.
--hsq
Specify the heritability. It defaults to 0.5.
--rep
Specify the replication for simulation. It defaults to 1.
--out
Specify the root of the output files.
Examples
gear simuqt-real --bfile test --hsq 0.25 --out test
gear simuqt-real --bfile test --hsq 0.2 --effect-file eff.txt --out test
*.phe: there are three columns included. The first two columns are family id, and individual id. The 3rd column is phenotypic value. When replication is bigger than 1, from the 3rd column represents phenotypic values for each replication.
*.breed: genotypic values for the simulated population.
*.rnd: there are three columns included. 1st is the marker name, 2nd is the reference allele, the 3rd column is its additive effect.
*.add: the genotype in additive model coding scheme.