You must specify a path to the directory containing Stacks output files.
genotypes 1.35
genotypes -b batch_id -P path [-r min] [-m min] [-t map_type -o type] [-B blacklist] [-W whitelist] [-c] [-s] [-e renz] [-v] [-h]
  b: Batch ID to examine when exporting from the catalog.
  r: minimum number of progeny required to print a marker.
  c: make automated corrections to the data.
  P: path to the Stacks output files.
  t: map type to write. 'CP', 'DH', 'F2', 'BC1' and 'GEN' are the currently supported map types.
  o: output file type to write, 'joinmap', 'onemap', 'rqtl', and 'genomic' are currently supported.
  m: specify a minimum stack depth required before exporting a locus in a particular individual.
  s: output a file to import results into an SQL database.
  B: specify a file containing Blacklisted markers to be excluded from the export.
  W: specify a file containign Whitelisted markers to include in the export.
  e: restriction enzyme, required if generating 'genomic' output.
  v: print program version.
  h: display this help messsage.
  Filtering options:
    --lnl_lim [num]: filter loci with log likelihood values below this threshold.
  Automated corrections options:
    --min_hom_seqs: minimum number of reads required at a stack to call a homozygous genotype (default 5).
    --min_het_seqs: below this minor allele frequency a stack is called a homozygote, above it (but below --max_het_seqs) it is called unknown (default 0.05).
    --max_het_seqs: minimum frequency of minor allele to call a heterozygote (default 0.1).
  Manual corrections options:
    --cor_path <path>: path to file containing manual genotype corrections from a Stacks SQL database to incorporate into output.