SAMBAMBA-INDEX(1)

SAMBAMBA-INDEX(1) — the manual page, but make it make sense 💅

okay bestie, so this is the sambamba-index(1) manual page, and honestly? it's a short one. which is great news for us because it means you'll actually remember it. 🎀

✨ NAME ✨

sambamba-index — the tool that builds standard index files for BAM data. that's it, that's the whole job, and it does it beautifully. 👑

🌸 SYNOPSIS 🌸

sambamba index [-p|--show-progress] [-t|--nthreads=NTHREADS] <input.bam>
[<output.bai>]

copy that exactly, don't freestyle it. 💖

🦋 DESCRIPTION 🦋

sambamba index builds an index for a BAM file that's sorted by coordinate. and why do we care?? because this step is required for effective region querying in most of the tools that work with BAM data. no index, no region queries, no slay. that's just the vibe. 😤

So where does the index go, you ask? by default it gets written to a file with the same filename except with .bai tacked onto the end. cute, right? but here's the thing — you're not stuck with that. you can absolutely override the default by handing over the output filename you actually want as an optional command-line argument. main character energy: you decide. ✨

💖 OPTIONS 💖

• -p, --show-progress — shows a wget-like progressbar over in STDERR. so you can sit there and watch it do its thing instead of wondering if it's frozen. we've all been there. 🫶
• -t, --nthreads=NTHREADS — the number of threads to use. more threads, more friends helping. 🔥

🌈 EXAMPLES 🌈

build an index file example.bam.bai given a sorted BAM file example.bam:

$ sambamba index example.bam

build the index file at a custom location AND show progress, because we love transparency:

$ sambamba index --show-progress example.bam /tmp/example.bam.bai

see? iconic behaviour. no notes. 💅

🎀 SEE ALSO 🎀

want the lore on how the original samtools INDEX behaves? go check out the samtools documentation, fr fr:

http://samtools.sourceforge.net/samtools.shtml

and that's a wrap, bestie!! this page is from the 2016-10-24 era, straight out of the SAMBAMBA-INDEX(1) manual. now go index something and be great. 🧚💜