samtools-flags(1)

📦
version 1.24 · 10 versions
, in epel 10, nixpkgs unstable

💅 samtools-flags(1) — the manual page, but make it make sense

okay bestie, welcome to the samtools-flags(1) page — yes that's the real manual name, yes it's giving reference-doc energy, and yes we're gonna get through it together 🫶

✨ NAME ✨

samtools flags — the little translator that converts between textual and numeric flag representation. that's it. that's the whole job. and it ate 💅

🌸 SYNOPSIS 🌸

samtools flags FLAGS...

🦋 DESCRIPTION 🦋

okay so real talk: this command converts between textual and numeric flag representation. same info, two outfits — one's a number, one's a name, and it slays at both 💖

each FLAGS argument can be either:

  • an integer (in decimal, hexadecimal, or octal, so go off with whatever base you vibe with) representing a combination of the numeric flag values listed below, or
  • a comma-separated string NAME,...,NAME representing a combination of the flag names listed below.

like, either flavor works. no cap. 🧚

FLAGS:

  • 0x1 — PAIRED — paired-end (or multiple-segment) sequencing technology 🌈
  • 0x2 — PROPER_PAIR — each segment properly aligned according to the aligner ✨
  • 0x4 — UNMAP — segment unmapped 💀
  • 0x8 — MUNMAP — next segment in the template unmapped 😭
  • 0x10 — REVERSE — SEQ is reverse complemented 🔥
  • 0x20 — MREVERSE — SEQ of the next segment in the template is reverse complemented 🔥
  • 0x40 — READ1 — the first segment in the template 👑
  • 0x80 — READ2 — the last segment in the template 👑
  • 0x100 — SECONDARY — secondary alignment ⭐
  • 0x200 — QCFAIL — not passing quality controls 🙈
  • 0x400 — DUP — PCR or optical duplicate 🍓
  • 0x800 — SUPPLEMENTARY — supplementary alignment 🎀

those are exactly the values, hex and all — don't come for me, I copied them character for character 💜

🎀 AUTHOR 🎀

written by Petr Danacek from the Sanger Institute. king behavior, honestly 👑

🌟 SEE ALSO 🌟

and that's the page!! 🦋 this was samtools-1.24, dated 9 July 2026 — go forth and decode your flags, bestie, iykyk 💅✨

📦 where this page comes from