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

COMPADRE computation (new)
  --segment_data       Shared segments data in ERSA format
  --port_number        Port number for additional Python computation (default: 6000)

Required for prePRIMUS, IMUS, and PR (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 file extensions;
                       behaves like PLINK's --file (requires --genome)
  --genome             Read in the --file and calculate IBD estimates using PLINK

General options:
  -t, --rel_threshold  Set the minimum relatedness for two people (default = 0.1)
  --degree_rel_cutoff  Set the maximum degree of relatedness (default = 3)
  -o, --output_dir     Specify the output directory for results 
                       (default = [PATH_TO_IBD_FILE]_PRIMUS/)
  -v, --verbose        Set verbosity level (0=none; 1=default; 2=more; 3=max)
  
prePRIMUS IBD estimation using PLINK (not included in lite version):
  --file               Path to PLINK formatted data without file extensions;
                       behaves like PLINK's --file (requires --genome)
  --genome             Read in the specified PLINK data file and calculate IBD estimates
                       using PLINK
  --plink_ex           Path to the plink executable (searched in environment by default)
  --smartpca_ex        Path to the EIGENSTRAT smartpca executable (searched in environment by default)
  --ref_pops           Comma-separated list of HapMap3 populations for reference allele freqs
                       (overrides default method)
  --no_automatic       Turn off automatic selection of HapMap3 populations for reference allele freqs
  --remove_AIMs        Automatically remove ancestry informative markers (default: off)
  --keep_AIMs          Do not remove ancestry informative markers (default: off)
  --internal_ref       Use the dataset in --file to get reference allele frequencies
  --alt_ref_stem       Path to PLINK formatted data (without file extensions) for allele frequencies
  --no_PCA_plot        Do not run smartpca or generate the PCA plot
  --keep_inter_files   Keep intermediate files used to create the IBD estimates with prePRIMUS

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

Pedigree reconstruction options:
  --no_PR              Do not reconstruct pedigrees (pedigree reconstruction runs by default)
  --max_gens           Maximum number of generations sampled in reconstructed pedigrees (default = no limit)
  --max_gen_gap        Maximum number of generations between two people having 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] with optional column specification
  --sex_file           Specify path to the file containing the sex of each sample
  --sexes              Like --sex_file but requires FILE=[file] with optional column specification
  --mito_matches       Path to mito matching status for each sample pair (requires FILE=[file])
  --y_matches          Path to y matching status for each sample pair (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; requires FILE=[file] with optional column specification
  --int_likelihood_cutoff  Initial minimum likelihood for a relationship (default = 0.1)

PADRE options:
  --run_padre          Run PADRE after standard reconstruction is complete