Config Variables:
{
"reference": "/path/to/reference", #Path to reference file
"famfile": "/path/to/familyfile", #Path to family file, formatted as FatherID,MotherID,ChildID
"data_dir": "/path/to/dnv/files", #Path to folder with vcf files
"out_dir": "/out_dir_name", #Path to outdir
"cramloc": "/file/of/cram/locations", #File with cram files locations, one per line
"lower": 0, #Number of allowed lower quality reads found in the parents
"upper": 0, #Number of allowed high quality reads found in the parents
"case_specific": "False", #check if low or high quality reads are found
"interval": "/path/to/capture_region/file", #capture file used for exons
"change": 40 #Defines how many basepairs from each end of the capture we will use to set low/high confidence regions
}