Hist_pop_QMSim.prm

/*******************************
  **     Global parameters     **
  *******************************/
  title = "Simulation historical population";
nrep  = 1;                    //Number of replicates
h2    = 0.8;                  //Heritability
qtlh2 = 0.0;                  //QTL heritability ???
phvar = 1.0;                  //Phenotypic variance
  
  /*******************************
    **   Historical population   **
    *******************************/
    begin_hp;
    hg_size = 100 [0]  
               100 [95]
               1000 [100];      //Size of the historical generations (with effective population size Ne)
   nmlhg   = 50;              //Number of males in the last generation
   nmfhg   = 50;              // Number of males in the first generation 
  end_hp;
  
  /*******************************
    **        Populations        **
    *******************************/
    begin_pop = "p1";
     begin_founder;
       male [n = 50, pop = "hp", select = rnd];
       female [n = 500, pop = "hp", select= rnd];
     end_founder;
     ng = 5;
     ls = 2;          //Litter size
     pmp = 0.5 /fix; //Proportion of male progeny
     md = rnd;       //Mating design (control of inbreeding) ;rnd, rnd_ug, minf, maxf, p_assort, n_assort
     sd = rnd;       //Selection design; rnd, phen, tbv and ebv
     ebv_est = blup ; // Breeding value estimation method; The best linear unbiased prediction (BLUP) of breeding values
     
      begin_popoutput;
       data;
       stat;   //Save brief statistics on simulated data
       genotype /snp_code ;
       allele_freq;   //Save allele frequencies
       ld;          //Save linkage disequilibrium stat
     end_popoutput;
     
    end_pop;
  
  /*******************************
    **          Genome           **
    *******************************/
    begin_genome;
    
      begin_chr = 30;
         chrlen = 100;     //Chromosome length (cM)
         nmloci = 300;     //Number of markers 9000/30
         mpos   = rnd;     //Marker positions
         nma    = all 2;    //Number of marker alleles
         maf    = eql;     //Marker allele frequencies
         nqloci = 90;         //Number of QTL 90 990 9990 60000
         qpos   = rnd;       //QTL positions
         nqa    = all 2;     //Number of QTL alleles
         qaf    = eql;       //QTL allele frequencies
         qae    = rndg 0.4;  //QTL allele effects % effects are sampled from gamma distribution
     end_chr;
      mmutr  = 2.5e-8 /recurrent;      // Marker mutation rate
      qmutr  = 2.5e-8;     //QTL mutation rate
      r_mpos_g; //Randomize marker positions across genome
      r_qpos_g; //Randomize QTL positions across genome
  end_genome;
  
  /*******************************
    **       Output options      **
    *******************************/
    begin_output;
     linkage_map; // Marker and QTL linkage map (GWAS)
     allele_effect;
    end_output;