BAMTOOLS(1)

📦
version 2.5.3 · 2 versions
, in ubuntu resolute, ubuntu stonking

💅 BAMTOOLS 💅

okay so bestie, welcome to the bamtools manual page — this is the User Commands section, and yes, it's giving main character energy for your whole bioinformatics pipeline. pull up a chair 🫶

✨ NAME ✨

bamtools — the toolkit for manipulating BAM (genome alignment) files. that's it. that's the whole vibe. 💖

🌸 SYNOPSIS 🌸

bamtools [--help] COMMAND [ARGS]

🦋 DESCRIPTION 🦋

BamTools is literally here to facilitate research analysis and data management using BAM files. no cap.

the way it carries the enormous amount of data produced by current sequencing technologies… like, that data is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research. so yeah, bamtools said "not on my watch" and handled it. periodt. 👑

✨ OPTIONS ✨

so these aren't your classic -a style flags, bestie — these are COMMANDS. each one is its own little icon. here's the full roster, no skips, no cuts 💅

  • convert — converts between BAM and a number of other formats. glow-up for your file types ✨
  • count — prints number of alignments in BAM file(s). just a lil headcount, nbd 🔢
  • coverage — prints coverage statistics from the input BAM file. stats girlies rise 🫶
  • filter — filters BAM file(s) by user-specified criteria. you decide what stays, you decide what goes 💅
  • header — prints BAM header information. the lore, basically 📜
  • index — generates index for BAM file. so you can find things fast, iykyk ⭐
  • merge — merge multiple BAM files into single file. many become one, iconic 🌈
  • random — select random alignments from existing BAM file(s), intended more as a testing tool. lowkey a testing tool, highkey chaotic 🎲
  • resolve — resolves paired-end reads (marking the IsProperPair flag as needed). matchmaking fr fr 💖
  • revert — removes duplicate marks and restores original base qualities. undo, but make it science 🧚
  • sort — sorts the BAM file according to some criteria. putting things in order, a to z, alphabetized, chef's kiss 🎀
  • split — splits a BAM file on user-specified property, creating a new BAM output file for each value found. one file becomes many, very demure 🌸
  • stats — prints some basic statistics from input BAM file(s). the numbers, the numbers, the numbers 📊
also bestie, for real: see 'bamtools help COMMAND' for more information on a specific command. don't just guess, go read the deets 💜

and that's the whole page!! this was bamtools 2.5.3+dfsg, written down in September 2025, and it is — and i say this with my whole chest — BAMTOOLS(1). slay, bye bestie 💅✨🎀🦋

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