popInf.config.json

{
  "_comment_sample_info": "This section of the .json file asks for sample information",
  "ref_panel_pop_info_path": "/PopInf/Sample_Information/ThousandGenomesSamples_AdmxRm.txt",
  "unkn_panel_pop_info_path": "/PopInf/Sample_Information/GTExSamples.txt",
  
  "_comment_general_options": "This section of the .json file asks for information needed to run popInf regardelss of what chromosomes you choose to analyze",
  "Autosomes_Yes_or_No": "N",
  "ref_path": "/mnt/storage/SAYRES/REFERENCE_GENOMES/hs37d5/hs37d5.fa",
  "genotype_call_rate_threshold": "0.98",
  
  "_comment_autosomes": "This section of the .json file asks for information needed for the autosomes if they are to be analyzed",
  "vcf_ref_panel_path": "/PopInf/Reference_Panel/",
  "vcf_ref_panel_prefix": "chr",
  "vcf_ref_panel_suffix": "_10000genomes_selected_individuals.vcf",
  "vcf_unknown_set_path": "/PopInf/Unknown_Samples/",
  "vcf_unknown_set_prefix": "chr",
  "vcf_unknown_set_suffix": "_unknown_panel.recode.vcf",
  "chromosome": ["1", "2", "3", "4", "5", "6", "7", 
                 "8", "9", "10", "11", "12", "13", "14", 
                 "15", "16", "17", "18", "19", "20", "21", "22"],
  
  "_comment_chrX": "This section of the .json file asks for information needed for the analysis of the X chromosome",
  "vcf_ref_panel_path_X": "/PopInf/Reference_Panel/",
  "vcf_ref_panel_file": "chrX_10000genomes_selected_individuals.vcf",
  "vcf_unknown_set_path_X": "/PopInf/Unknown_Samples/",
  "vcf_unknown_set_file": "chrX_unknown_panel.recode.vcf",
  "X_chr_coordinates": "/PopInf/X_chromosome_regions_XTR_hg19.bed"
}