R语言代码有兴趣可以了解一下：

###########genotype#############################
genotype<-function(){
count<-0
	
	
if (population_structure=="RIL"){
x<-runif(1) 
if (x<=0.5){
count<-1
}else{
count<-0
}	
		
}else{
for(i in 1:2){
x<-runif(1) 
if (x<=0.5){
number<-0.5
}else{
number<-0
}	
if(number == 0.5){
count<- count+0.5
}
}
}
return(count)
}
############################################################

###########caluclate of genotype ratio#########################
individuals_genotype<-function(number_of_total_individuals){
	
ratio_of_genotype<-c()
for(i in 1:number_of_total_individuals){
ratio_of_genotype<-c(ratio_of_genotype,genotype())
		
}
return(mean(ratio_of_genotype))	
}
############################################################

###########SNP_index_caluclation#########################
snp_index<-function(read_depth,ratio_of_genotype_in_the_population){
x1<-rbinom(1,read_depth,ratio_of_genotype_in_the_population)
return(x1/read_depth)	
}
############################################################
####################################

####################################
Arg<-commandArgs(TRUE)
###########input###############################################
population_structure<-"F2"
individual_analysis<- c(Arg[1])
reprication<-c(Arg[2])
filter_value<-c(Arg[3])
depth_analysis<-c(1:300)
###########input###############################################



for (key_individual in individual_analysis){
   individual_number<-key_individual
    
    depth_data<-c()
    p_h_data_95<-c()
    p_h_data_99<-c()
    for (key_depth in depth_analysis){
            depth_data<-c(depth_data,key_depth)
            depth<-key_depth
        sum_snp_index<-c()    
        for(i in 1:reprication){    
        ##########gene_frequency######################
ratio_of_genotype_in_the_population<-individuals_genotype(key_individual)
a_snp_index<-snp_index(key_depth,ratio_of_genotype_in_the_population)
if(a_snp_index >= filter_value){
sum_snp_index<-c(sum_snp_index,a_snp_index)
}
##########gene_frequency######################
        }
        order_sum_snp_index<-sort(sum_snp_index)
        length_sum_snp_index<-length(sum_snp_index)
        ##########snp_index_probabirity_0.05######################       
snp_cutoff_up_0.95<-order_sum_snp_index[ceiling(0.95*length_sum_snp_index)]
        p_h_data_95<-c(p_h_data_95,snp_cutoff_up_0.95)   
        ##########snp_index_probabirity_0.05######################
        
        ##########snp_index_probabirity_0.01###################### 
        
        if (ceiling(0.99*length_sum_snp_index)<length_sum_snp_index){
snp_cutoff_up_0.99<-order_sum_snp_index[ceiling(0.99*length_sum_snp_index)]
}else{
snp_cutoff_up_0.99<-order_sum_snp_index[length_sum_snp_index]
}
        p_h_data_99<-c(p_h_data_99,snp_cutoff_up_0.99) 
        ##########snp_index_probabirity_0.01######################      
               
            
     
     
    }
    
        
    FINAL_DATA<-data.frame(DEPTH=depth_data,P_H_95=p_h_data_95,P_H_99=p_h_data_99)
    
    table_name<-paste("./",individual_number,sep="")
    table_name<-paste(table_name,"individuals.txt",sep="")
    write.table(FINAL_DATA,table_name,sep="\t", quote=F, append=F,row.name=F)
    
}