POPSTATS(1)

📦
version 1.0.12 · 3 versions
, in debian trixie, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 NAME 💖

popStats — general population genetic statistics for each SNP, and honestly? She ate. 💅 This is the manual page for popStats from the vcflib crew (yes, that's POPSTATS(1) bestie, iykyk).

✨ SYNOPSIS ✨

popStat –type PL –target 0,1,2,3,4,5,6,7 –file my.vcf

🦋 DESCRIPTION 🦋

popStats gives you general population genetic statistics for each SNP. That's the whole job. One SNP at a time, stats delivered, no drama. 🌸

🎀 OPTIONS 🎀

okay so the main character here calculates basic population statistics at bi-allelic sites. Let's get into it, fr fr:

  • The allele frequency is the number of non-reference alleles divided by the total number of alleles.
  • The expected heterozygosity is 2*p*q, where p is the non-reference allele frequency and q is 1-p.
  • The observed heterozygosity is the fraction of 0/1 genotypes out of all genotypes.
  • The inbreeding coefficient, Fis, is the relative heterozygosity of each individual vs. compared to the target group.

Output : 9 columns :

  1. seqid
  2. position
  3. target allele frequency
  4. expected heterozygosity
  5. observed heterozygosity
  6. number of hets
  7. number of homozygous ref
  8. number of homozygous alt
  9. target Fis

and now the flags, bestie — every single one, no skipping 💖:

  • -t, --target — required ✨ a zero based comma separated list of target individuals corresponding to VCF columns
  • -f, --file — required ✨ proper formatted VCF
  • -y, --type — required ✨ genotype likelihood format; genotype : GL, PL, GP
  • -r, --region — optional ✨ a tabix compliant region : chr1:1-1000 or chr1

Type: statistics

⭐ EXIT VALUES ⭐

  • 0 — Success 🎉 (the good ending, she slayed)
  • not 0 — Failure 😭 (vibe check failed)

🌸 SEE ALSO 🌸

vcflib(1) — go read the whole family, they're all iconic 👑

💜 OTHER 💜

LICENSE

Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2024 (C) Pjotr Prins.

AUTHORS

Erik Garrison and vcflib contributors.

and that's the tea 🍓 — this was popStats from vcflib, manual page POPSTATS(1). go run it on your VCF, you've got this 💖✨🦋

📦 where this page comes from