configure.txt

gene_level		#Mode: chrom_level,gene_level
/Users/kenhsu/Dropbox/Mac/Desktop/311/高粱/master_thesis/WGSample/Out/30_vcf/qtlseq.ann.vcf	#vcf file path
parent_V9	#parent_name
bulk1_1_10_4,bulk1_1_10_6,bulk1_1_10_14,bulk1_19_22_12,bulk1_19_24_12,bulk1_19_24_15,bulk2_2_16_18,bulk2_2_16_6,bulk2_6_13_14,bulk2_6_13_19,bulk2_15_1_20,bulk2_15_1_25,bulk2_15_1_15		#Order and ind want to show in the plot
/Users/kenhsu/Dropbox/Mac/Desktop/311/高粱/master_thesis/WGSample/Out/10_ref/Sbicolor_454_v3.0.1.fa		#file path to reference genome
Chr01:6699580-6708049	#Range want to show
/Users/kenhsu/Dropbox/Mac/Desktop/MolecularBreeding/New_graph/		#Output plot path
		#skip variants, only apply to gene_level
/Users/kenhsu/Dropbox/Mac/Desktop/MolecularBreeding/WGS Data procession/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.59.gff3		#Here is gtf file path to check each transcript flanking, but please check the gene name or id should be coherent, and please use gff3 here
0.1		#max missing rate of variants in gene/chromosome level