###To convert prettybase or HapMap genotype format into genotype format used by mPopTag

##Basic options
#data format; 1: HapMap; 2: prettybase;  
-format: 1
#directory for output 
-output_dir: indir
#maximum percentage of missing genotypes allowed for inclusion of a SNP
-max_miss: 0.9
#display program progress? 1: yes; 0: no;
-verbose: 1


## For prettybase format
#individual list and associated populations. This file should be put in direcoty specified by input_dir above
-ind_list: p2pid.txt
#diretory for input files
-pretty_dir: indir/prettybase
#Genotype file list; This file should be put in directory specified by pretty_dir above
-pretty_list: list


## For HapMap format
#only use independent individuals? 1: yes; 2: no. If yes, genotypes for only 60 parents in YRI or CEU will be converted. 1 was recommended.
-independent: 1
#diretory for input files
-hapmap_dir: indir/hapmap
#Genotype file list and associated population and gene list;This file should be put in directory specified by input_dir above
-hapmap_list: list

