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 (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
  --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 to be considered related (default: 3)
  -o, --output_dir            Specify path to 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 options:
  --file                      Path to PLINK formatted data (requires --genome)
  --genome                    Calculate IBD estimates using PLINK
  --plink_ex                  Path to the plink executable file
  --ref_pops                  Comma-separated 1000 Genomes populations for allele freqs
  --no_automatic              Disable automatic selection of reference allele freqs
  --remove_AIMs               Remove ancestry informative markers (off by default)
  --keep_AIMs                 Keep ancestry informative markers (off by default)
  --internal_ref              Use --file dataset for reference allele freqs
  --alt_ref_stem              Path to PLINK formatted data used for allele freqs
  --keep_inter_files          Keep intermediate files
  --min_pihat_threshold       Minimum pi-hat threshold for --genome calculation
  --max_memory                Memory (MB) to use in prePRIMUS PLINK commands

IMUS (maximum unrelated set) options:
  --no_IMUS                   Do not run IMUS (default: run)
  --missing_val               Missing data marker in IBD file
  -s, --size                  Weight on set size
  --high_btrait               Binary trait file to weight higher values
  --low_btrait                Binary trait file to weight lower values
  --high_qtrait               Quantitative trait file to weight higher values
  --low_qtrait                Quantitative trait file to weight lower values
  --mean_qtrait               Quantitative trait file to weight toward mean
  --tails_qtrait              Quantitative trait file to weight against middle values

Pedigree reconstruction (PR) options:
  --no_PR                     Skip pedigree reconstruction
  --max_gens                  Max generations in pedigree (default: no limit)
  --max_gen_gap               Max generations between parents and children (default: 0)
  --age_file                  File with sample ages
  --ages                      Like --age_file, requires FILE=[file]
  --sex_file                  File with sample sex
  --sexes                     Like --sex_file, requires FILE=[file]
  --mito_matches              File with mitochondrial match status
  --y_matches                 File with Y chromosome match status
  --MT_error_rate             Max MT mismatch proportion to call a match
  --Y_error_rate              Max Y mismatch proportion to call a match
  --affection_file            File with affection status per sample
  --affections                Like --affection_file, requires FILE=[file]
  --int_likelihood_cutoff     Minimum likelihood for relationships (default: 0.1)

ERSA options:
  --min_cm                    Minimum segment size (default: 5 cM)
  --max_cm                    Max segment size for exponential distribution (default: 10.0)
  --max_meioses               Max meioses to consider (default: 40)
  --rec_per_meioses           Expected recombinations per meioses (default: 35.2548101)
  --ascertained_chromosome    Chromosome number of disease locus
  --ascertained_position      Position of disease locus
  --control_files             GERMLINE or Beagle fibd files for population control
  --control_sample_size       Control sample size
  --exp_mean                  Mean of exponential segment size distribution (default: 3.197036753)
  --pois_mean                 Mean Poisson distribution of segment count (default: 13.73)
  --pair_file                 Restrict pairwise comparisons to IDs in this file
  --single_pair               Restrict comparisons to a single pair (id1:id2)
  --number_of_ancestors       Limit to 0/1/2 parents (default varies)
  --number_of_chromosomes     Number of chromosomes (default: 22)
  --parent_offspring_option   Evaluate PO/sibling based on IBD1 (default: true)
  --parent_offspring_zscore   Z-score threshold for sibling vs PO (default: 2.33)
  --adjust_pop_dist           Adjust for recent ancestry (default: false)
  --confidence_level          CI level around estimated relationship (default: 0.95)
  --mask_common_shared_regions  Mask common regions (default: false)
  --mask_region_cross_length  Segment length past mask to avoid truncation (default: 1000000)
  --mask_region_file          File of masked chromosomal regions
  --mask_region_threshold     Observed vs. expected segment sharing ratio threshold
  --mask_region_sim_count     Simulations for null sharing distribution
  --recombination_files       Genetic distances (required with Beagle input)
  --beagle_markers_files      Beagle marker files, one per chromosome (ex: chr*beagle.marker)