###lines beginning with "#" are annotation lines
###Parameter values should be given after colon ":" sign; Words before colon are key words and should not be changed
## run options
#Command to run R in your computer, include abosolute path for R if it is not in your system default path
-Rcommand: R

##Basic options
#task? 0:LD tag selection only;  1: selection and evaluation; 2: tag SNPs evaluation only
-task: 1
#selection method. 1:greedy; 2:exhaustive search for single population or two-stage exhaustive search for multi-pop; 3 hybrid;
-selection_method: 1
#Number of populations and the file names for each population data
#-n_pop: 4, african,asian,ceu,hisp
-n_pop: 3, african,asian,ceu
#directory for input file
-input_dir: indir
#directory for output 
-output_dir: outdir
#LD method 1:CLD, 2:r^2
-LD_method: 2
#minimum number of informative genotype pairs required between 2 SNPs to calculate a valid LD value between them
-Vgenopair: 5
#LD threshold
-cutoff_LD: 0.8
#maximum distance between SNPs for calculation of LD (unit: base pair)
-max_distance:  500000


##Options for tag SNP selection
#the range of SNP minor allele frequency for tag SNP selection. []:include upper or lower limit; (): not include upper or lower limit
-selection_maf: [0.05,0.5]
#Minimum number of SNPs tagged by a tag SNPs, must great or equal to 1
-minimum: 1


##Options for tag SNP evaluation
#the range of SNP minor allele frequency for tag SNP evaluation. []:include upper or lower limit; (): not include upper or lower limit
-evaluation_maf: [0.05,0.5]


##Options for exhaustive or two-stage exhaustive search algorithm
#max number of tries for exhaustive search 
-maxtry: 1000000


##Options for additional information
#Required tag SNPs list; 0: no, 1: yes; provide file name if yes; !!!this parameter must be set if task 2 was selected
-include_snp: 0, include.txt 
#-include_snp: 1, multipop_tags.txt 
#excluded tag SNPs list; 0: no, 1: yes; provide file name if yes
-exclude_snp: 0, exclude.txt 
#SNP design score; 0: no, 1: yes; provide file name if yes
-score: 0, score.csv
#SNP design score cutoff; 0: no, 1: yes; provide cutoff value and score file if yes
-scut: 0, 0.6
#SNP list for non-synonymous SNPs; 0: no, 1: yes; provide file name if yes
-csnp: 0, nssnp 


##Options for genotype or LD figures
#output figure file; 0: no figure; 1: genotype figure; 2: LD figure;  3:both figures. 
-figure: 3
#sort SNP by 1: genotype similarity; 2: LD similarity; 3: chromosome position
-sort_snp: 2
#show LD bin and Ave.r2 in figure; 0:no 1:yes
-track_ldbin: 1
#show track for SNP preference score in figure; 0:no 1:yes, followed by score name
-track_score: 0,SNP_Design_Score
#show relative SNP tagging ability track; 0:no 1:yes
-track_tagpower: 1
#show minor allele frequency track in figure; 0:no 1:yes, 
-track_maf: 1
#mark common or rare SNPs? 0:no 1:yes, followed by the cutoff value of MAF for classification of common SNPs
-common_rare: 1,0.05
#show flags for nonsynonymous SNPs in figure; 0:no 1:yes
-track_nssnp: 0
#show major/minor allele for each SNPs; 0:no 1:yes
-track_allele: 1
#Figure border, 1:white; 2:NA
-bcol: 1
#Figure type; 1: pdf; 2:eps. 
-figtype: 1
#mark SNP rsID with genomic context
-ctextk: 0, ctext
#physical chromosome position track
-track_pos: 1
