You must specify a path to the directory containing Stacks output files.
populations 1.35
populations -b batch_id -P path -M path [-r min] [-m min] [-B blacklist] [-W whitelist] [-s] [-e renz] [-t threads] [-v] [-h]
  b: Batch ID to examine when exporting from the catalog.
  P: path to the Stacks output files.
  M: path to the population map, a tab separated file describing which individuals belong in which population.
  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 containing Whitelisted markers to include in the export.
  e: restriction enzyme, required if generating 'genomic' output.
  t: number of threads to run in parallel sections of code.
  v: print program version.
  h: display this help messsage.

  Merging and Phasing:
    --merge_sites: merge loci that were produced from the same restriction enzyme cutsite (requires reference-aligned data).
    --merge_prune_lim: when merging adjacent loci, if at least X% samples posses both loci prune the remaining samples out of the analysis.
  Data Filtering:
    r: minimum percentage of individuals in a population required to process a locus for that population.
    p: minimum number of populations a locus must be present in to process a locus.
    m: specify a minimum stack depth required for individuals at a locus.
    f: specify a correction to be applied to Fst values: 'p_value', 'bonferroni_win', or 'bonferroni_gen'.
    --min_maf: specify a minimum minor allele frequency required to process a nucleotide site at a locus (0 < min_maf < 0.5).
    --max_obs_het: specify a maximum observed heterozygosity required to process a nucleotide site at a locus.
    --p_value_cutoff [num]: required p-value to keep an Fst measurement (0.05 by default). Also used as base for Bonferroni correction.
    --lnl_lim [num]: filter loci with log likelihood values below this threshold.
    --write_single_snp: restrict data analysis to only the first SNP per locus.
    --write_random_snp: restrict data analysis to one random SNP per locus.

  Fstats:
    --fstats: enable SNP and haplotype-based F statistics.

  Kernel-smoothing algorithm:
    k: enable kernel-smoothed Pi, Fis, Fst, Fst', and Phi_st calculations.
    --window_size [num]: distance over which to average values (sigma, default 150,000bp; window is 3sigma in length).

  Bootstrap Resampling:
    --bootstrap: turn on boostrap resampling for all smoothed statistics.
    --bootstrap_pifis: turn on boostrap resampling for smoothed SNP-based Pi and Fis calculations.
    --bootstrap_fst: turn on boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs.
    --bootstrap_div: turn on boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes.
    --bootstrap_phist: turn on boostrap resampling for smoothed Phi_st calculations based on haplotypes.
    --bootstrap_reps [num]: number of bootstrap resamplings to calculate (default 100).
    --bootstrap_wl [path]: only bootstrap loci contained in this whitelist.

  File ouput options:
    --ordered_export: if data is reference aligned, exports will be ordered; only a single representative of each overlapping site.
    --genomic: output each nucleotide position (fixed or polymorphic) in all population members to a file.
    --fasta: output full sequence for each unique haplotype, from each sample locus in FASTA format, regardless of plausibility.
    --fasta_strict: output full sequence for each haplotype, from each sample locus in FASTA format, only for biologically plausible loci.
    --vcf: output SNPs in Variant Call Format (VCF).
    --vcf_haplotypes: output haplotypes in Variant Call Format (VCF).
    --genepop: output results in GenePop format.
    --structure: output results in Structure format.
    --phase: output genotypes in PHASE format.
    --fastphase: output genotypes in fastPHASE format.
    --beagle: output genotypes in Beagle format.
    --beagle_phased: output haplotypes in Beagle format.
    --plink: output genotypes in PLINK format.
    --hzar: output genotypes in Hybrid Zone Analysis using R (HZAR) format.
    --phylip: output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction.
    --phylip_var: include variable sites in the phylip output encoded using IUPAC notation.
    --phylip_var_all: include all sequence as well as variable sites in the phylip output encoded using IUPAC notation.
    --treemix: output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard).

  Debugging:
    --verbose: turn on additional logging.
    --log_fst_comp: log components of Fst/Phi_st calculations to a file.