-fst_correction - specify a correction to be applied to Fst values: 'p_value'.-fstats - enable SNP and haplotype-based F statistics.-hwe - calculate divergence from Hardy-Weinberg equilibrium for each locus.-W,-whitelist - path to a file containing Whitelisted markers to include in the export.-B,-blacklist - path to a file containing Blacklisted markers to be excluded from the export.-write-random-snp - restrict data analysis to one random SNP per locus.-write-single-snp - restrict data analysis to only the first SNP per locus.-max-obs-het - specify a maximum observed heterozygosity required to process a nucleotide site at a locus (applied to the metapopulation).-min-mac - specify a minimum minor allele count required to process a SNP (applied to the metapopulation).-min-maf - specify a minimum minor allele frequency required to process a nucleotide site at a locus (0 -H,-filter-haplotype-wise - apply the above filters haplotype wise (unshared SNPs will be pruned to reduce haplotype-wise missing data).-R,-min-samples-overall - minimum percentage of individuals across populations required to process a locus.-r,-min-samples-per-pop - minimum percentage of individuals in a population required to process a locus for that population.-p,-min-populations - minimum number of populations a locus must be present in to process a locus.-t,-threads - number of threads to run in parallel sections of code.-M,-popmap - path to a population map.(Required by -V otherwise defaults to value of -P.) -O,-out_path - path to a directory where to white the output files.-V,-in_vcf - path to an input VCF file.-P,-in_path - path to the directory containing the Stacks files.Populations -P dir (filters) ]] (output formats) populations -V vcf -O dir (filters) ]] (output formats) For more information on whitelists and blacklists, see the manual. Whitelists and blacklists if you want to include a specific list of loci (or exclude a specific The populations program provides strong filtering options to only include loci or variant sites that occur atĬertain frequencies in each population or in the metapopulation.
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More information on how to specify a population map, see the manual. Population genetics statistics including haplotype diversity, Φ ST, and F ST’. The populations program can also compute a number of haplotype-based If a set of data is reference aligned, then a kernel-smoothed F ST will also beĬalculated. The populations program will compare all populations pairwise toĬompute F ST. Specifying which individuals belong to which population is submitted to the program and the program will thenĬalculate population genetics statistics such as expected/observed heterozygosity, π, and F IS at each
Of population genetics statistics as well as exporting a variety of standard output formats. The populations program will analyze a population of individual samples computing a number
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