text: import os
  import pandas as pd
  import datetime
  from timeit import default_timer as timer
  import argparse
  
  #Start timer
  start = timer()
  time = datetime.datetime.now().strftime("%Y-%m-%d: %H:%M")
  print "Start running script at: {0}".format(time)
  
  ###Parse arguments
  parser = argparse.ArgumentParser(description = "This script extracts the loci that were 'Callable' in all members in a parent-offspring trio These loci are extracted from bed files generated by GATKs CallableLoci.")
  parser.add_argument("-f", "--FILELIST", default = "/hpc/cog_bioinf/cuppen/project_data/Freek_SNV/FilelistFreek.txt", help = "The file list")
  parser.add_argument("-o", "--OUTPUT_PATH", default = "/hpc/cog_bioinf/cuppen/project_data/Freek_SNV", help = "The output path")
  parser.add_argument("-w", "--OVERWRITE", default = "False", help = "Overwrite the results if they already exist.")
  parser.add_argument("--SNPSIFT", default = "/hpc/local/CentOS7/cog_bioinf/snpEff_v4.1h/SnpSift.jar", help = "The location of the snpsift jar.")
  args = parser.parse_args()
  
  filelist = args.FILELIST
  outdir = "{0}/Callableregion_NrMendelViols".format(args.OUTPUT_PATH)
  snpsift = args.SNPSIFT
  
  #Create the file paths.
  folder = "{0}/Callableregion_NrMendelViols/TrueDenovo/SNVs".format(args.OUTPUT_PATH)
  manualcheck = "{0}/Manualcheck".format(folder)
  filteredonfreq = "{0}/Possibly_pathogenic/SNVs/Filteredonfreq".format(args.OUTPUT_PATH)
  
  dffiles = pd.read_csv(filelist, sep = "\t", header = 0)
  childrowsf = dffiles["Name"].str.contains("Child|child")
  dffiles = dffiles[childrowsf]
  dffiles["vcf"] = folder + "/" + dffiles["Sample"] + "_Truedenovo.vcf"
  dffiles["vcf_f"] = filteredonfreq + "/" + dffiles["Sample"] + "_freqfilter.vcf"
  
  
  #Filter the vcfs on gnomAD and GoNLv5 databases
  for index, row in dffiles.iterrows():
  	sample, vcf, vcf_f = row[["Sample", "vcf", "vcf_f"]].values.tolist()
  	if os.path.isfile(vcf) and (not os.path.isfile(vcf_f) or args.OVERWRITE == "true"):
  		command = """java -Xmx4G -jar {0} filter "!( gnomAD_AC > 1 ) & !( GoNLv5_AC > 1 ) & !( PON_COUNT > 1 )" {1} > {2}""".format(snpsift, vcf, vcf_f)
  		os.system(command)
  		print "Filtered out muts with a gnomAD or GoNLv5 allele count of more than 1 in sample: {0}".format(sample)
  		
  		
  #End timer		
  timeend = datetime.datetime.now().strftime("%Y-%m-%d: %H:%M")
  print "Finished running script at: {0}".format(timeend)
  end = timer()
  execution_time = int(end - start)
  execution_time = datetime.timedelta(seconds = execution_time)
  print "Elapsed time: {0}".format(execution_time)
  
  