#Path to a file that contains algorithm configurations
cfg_path=E:\BCL_STUDIO\sample\QTM\SimF2.cfg

#Wait for user intervention on algorithm completion
#instead of auto-terminating the process.
wait_on_finish=1

#Source data format:
#0 for QTLNetwork format(default)
#1 for QTL Cartographer OUT format
#2 for MapMarker/QTL format.
source_data_form=0

#Type of source file(s). 
#0 for solo txt file(default)
#1 for a pair of genotype and phenotype file
source_file_type=0

#Algorithm type 0=QTLNetwork Marker(QTM) 1=QTLNetwork SNP(QTS default).
algorithm_type=0

#Path to map source file which is essential for QTM but optional for QTS.
map_path=E:\BCL_STUDIO\sample\QTM\SimF2.map

#Path to txt source file which contains genotype & phenotype data needed by all types of algorithm.
txt_path=E:\BCL_STUDIO\sample\QTM\SimF2.txt

#Path to genotype  source file.
gen_path=

#Path to phenotype source file.
pno_path=

#Path to output report which by default equals to input path with changed extension ".pre".
output_report=

#Perform 2-dimensional scan to detect epistatic QTLs with no main effects 1 for yes and 0 for no.
_2D_scan=1

#The critical distance for grouping unit cM.
_critical_distance=50.000000

#If the marker number of a linkage group fall below this the linkage will be removed.
_critical_marker_number=3

#Define threshold window for distinguishing two QTLs on adjacent test statistic peaks.
_filter_window=10.000000

#Gibbs sampling size of MCMC procedure.
_Gibbs_sample_size=20000

#Grouping criteria 0 for p value and 1 for distance.
_grouping_criteria=0

#Map epistasis 1 for yes and 0 for no.
_map_epistasis=1

#Map function used for linkage group construction 0 for haldane and 1 for kosambi.
_map_function=1

#Map AD DA and DD effects in F2 or IF2 population 1 for yes and 0 for no.
_map_high_order_epistasis=1

#Maximum number of digits to display after decimal point for output values.
_max_decimal=4

#Output configuration setting 1 for yes and 0 for no.
_output_configuration=1

#Output residuals setting 1 for yes and 0 for no.
_output_residuals=0

#Output F plots for R 1 for yes and 0 for no.
_output_for_R=0

#Time of permutation shuffling set to 0 to disable permutation.
_Permutation_times=1000

#Probabilty Threshold for deciding significant QTL effects.
_SL_effect=0.050000

#Significant level (SL) for filtering markers.
_SL_filter_marker=0.050000

#Significant level (SL) for grouping.
_SL_grouping=0.050000

#Experimetal-wise significant level (SL) in candidate marker (or marker interaction) detection.
_SL_marker=0.050000

#Experimetal-wise significant level (SL) in putative QTL (or epistasis) detection.
_SL_QTL=0.050000

#Show F values when performing genome search 1 for yes and 0 for no.
_show_F_value=1

#Show all peaks when performing genome search 1 for yes and 0 for no.
_show_all_peaks=0

#Predict superior genotypes based on QTL effects 1 for yes and 0 for no.
_superior_genotype_prediction=1

#Markers falling into adjacent windows(positive and nagtive) of the testing interval
# will not be selected as cofactor. (Unit=cM)
_test_window=10.000000

#The space between two adjacent test point in genome scan. (Unit cM).
_walk_speed=1.000000