For usage and documentation:
  -h, --help		      Brief help message

Required options (one of the following):
  -p, --plink_ibd	    Specify path to a .genome IBD estimates file produced by PLINK
  -i, --input		      Specify path to an IBD estimates file and additional column information
  
  (or both):
  --file 		          Path to PLINK formatted data without the file extensions; behaves the same as in PLINK (requires --genome)
  --genome		        Read in --file and calculate IBD estimates using PLINK

COMPADRE options (new):
  --segment_data      Shared segments data in format readable by ERSA (see full documentation)
  --port_number       Port number for additional Python computation (default: 6000)
  --run_padre			    Run PADRE after standard pedigree reconstruction is complete

General options:
  -t, --rel_threshold	Set the minimum level of relatedness for two people to be considered related (default=0.1)
  --degree_rel_cutoff	Set the maximum degree of relatedness for two people to be considered related (default=3; i.e. 3rd degree relatives)
  -o, --output_dir	  Specify path to the output directory for all results(default=[PATH_TO_IBD_FILE]_PRIMUS/)
  -v, --verbose	      Set verbosity level (0=none; 1=default; 2=more; 3=max)

prePRIMUS IBD estimation options:
  --file 		          Path to PLINK formatted data without the file extensions; behaves the same as in PLINK (requires --genome)
  --genome		        Read in the specified PLINK formatted data file and calculate IBD estimates using PLINK
  --plink_ex		      Path to the plink executable file (searches environment variables by default)
  --ref_pops		      Comma separated list of 1000 Genomes populations used for reference allele freqs (overrides default method) 
  --no_automatic	    Turn off automatic selection of the HapMap3 populations for reference allele freqs (on by default)
  --remove_AIMs	      Automatically remove ancestry informative markers (off by default)
  --keep_AIMs		      Do not remove ancestry informative markers(off by default)
  --internal_ref	    Use the dataset provided in --file to get reference allele frequencies
  --alt_ref_stem	    Path to PLINK formatted data (no file extensions) used for allele frequencies
  --keep_inter_files	Keep intermediate files used to create the IBD estimates with prePRIMUS
  --min_pihat_threshold Set a minimum pi-hat threshold that will be used in the plink --genome calculation
  --max_memory		    Specify amount of memory to be used in PLINK prePRIMUS commands (in MB)

Identification of maximum unrelated set (IMUS) options:
  --no_IMUS		        Don't identify a maximum unrelated set (runs IMUS by default)
  --missing_val	      Set value that denotes missing data in IBD file
  -s, --size		      Specify to weight on set size (Default unless a binary trait is specified first)
  --high_btrait	      File with FID, IID, and binary trait to weight for the higher value
  --low_btrait		    File with FID, IID, and binary trait to weight for the lower value
  --high_qtrait	      File with FID, IID, and quantitative trait to weight for higher values
  --low_qtrait		    File with FID, IID, and quantitative trait to weight for lower values
  --mean_qtrait	      File with FID, IID, and quantitative trait to weight towards the mean value
  --tails_qtrait	    File with FID, IID, and quantitative trait to weight against the middle values

Pedigree reconstruction (PR) options:
  --no_PR		          Don't reconstruct pedigrees (runs pedigree reconstruction by default)
  --max_gens		      Max number of generations sampled in reconstructed pedigree (default = no limit)
  --max_gen_gap	      Max number of generations between two people that have a child (default = 0)
  --age_file		      Specify path to the file containing the age of each sample
  --ages		          Like --age_file but requires FILE=[file], optional specification of file columns
  --sex_file		      Specify path to the file containing the sex of each sample
  --sexes		          Like --sex_file but requires FILE=[file], optional specification of file columns
  --mito_matches	    Path to mito matching status for each pair of samples (requires FILE=[file])
  --y_matches		      Path to y matching status for each pair of samples (requires FILE=[file])
  --MT_error_rate	    Proportion of the MT sequence that must not match to be called a non-match
  --Y_error_rate	    Proportion of the Y sequence that must not match to be called a non-match
  --affection_file	  Specify path to the file containing the affection status of each sample
  --affections		    Like --affection_file; need FILE=[file], optional specification of file columns
  --int_likelihood_cutoff	Initial minimum likelihood for a relationship to reconstruction (default = 0.1)