SAMBAMBA-MERGE(1)

📦 version 1.0.1, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 SAMBAMBA-MERGE 💖

okay bestie, welcome to the sambamba-merge page of the manual — it's the one that lives in section 1, and it's literally just here to help you smoosh a bunch of BAM files together into one. no cap. 🫶

✨ NAME ✨

sambamba-merge — the tool for merging several BAM files into one. that's it. that's the whole job. iconic. 👑

✨ SYNOPSIS ✨

sambamba merge OPTIONS <output.bam> <input1.bam> <input2.bam> [...]

✨ DESCRIPTION ✨

so sambamba merge is what you reach for when you've got a whole squad of sorted BAM files and you want them to become one sorted BAM file. the way that this works is: the sorting order of all the files has to be the same, and whatever that order is, it gets maintained in the output file. like, it's not gonna re-sort your life for you, it just keeps the vibe consistent. 💅

SAM headers? merged automatically, same energy as the Picard merging tool. so you don't have to hand-craft anything, it just handles it. slay. ✨

✨ OPTIONS ✨

  • -t, --nthreads=NTHREADS — tell it how many threads to use for the compression/decompression tasks. more threads = more goblins working on it. 🧚
  • -l, --compression-level=COMPRESSION_LEVEL — set the compression level of the output file, as a number from 0 to 9. yes, a number. 0 through 9. those exact ones. 🙈
  • -H, --header — outputs only the merged header, to stdout, in SAM format — super handy for debugging purposes. and listen: when you use this, the other options are ignored. ignored!! they just don't get a turn. 💀
  • -p, --show-progress — shows a progressbar in STDERR, so you can watch the whole thing happen in real time instead of staring at a blank terminal like 👁️👄👁️. for more info on the original samtools MERGE behaviour, check out the samtools documentation at http://samtools.sourceforge.net/samtools.shtml
fr fr: the sorting order of every input file must match, or this whole plan falls apart. no cap.

and that's the page, bestie 🎀 this one came from February 2015 and it's filed under SAMBAMBA-MERGE(1) — go forth and merge, you absolute main character. 💜🌸🦋

📦 where this page comes from