SAMBAMBA-MILEUP(1)

✨ SAMBAMBA-MILEUP ✨

okay bestie, pull up a chair, we're doing the sambamba-mileup page from the SAMBAMBA-MILEUP(1) manual 💅 this is the one about making a pileup, and honestly? it's giving parallel-processing main character energy 🧚

🌸 NAME 🌸

<pink>sambamba-mileup</pink> — make a pileup. that's it, that's the whole name section, short and slay 💖

🦋 SYNOPSIS 🦋

sambamba mpileup OPTIONS <input1.bam> <input2.bam> [...] [--samtools
samtools mpileup args] [--bcftools bcftools args]

no cap, that's the exact shape of it. OPTIONS first, then as many .bam files as your little heart desires, then optionally the samtools args and optionally the bcftools args 🫶

👑 DESCRIPTION 👑

so basically it's a parallel version of samtools mpileup done in map-reduce fashion ✨ like, Sambamba splits your input BAM files into chunks and feeds them to samtools mpileup and, optionally, bcftools, all in parallel. iconic behaviour, honestly.

and the chunks are slightly overlapping so that variant calling should not be impacted by these manipulations. the results from all the multiple processes get combined as ordered output 🎀

also, named pipes are created in TMPDIR — yes queen, TMPDIR, remember that 👑

here's the tea though: sambamba mpileup relies on external tools and acts as a multi-core implementation of samtools + bcftools. so the following tools should be present in the PATH:

• samtools
• bcftools (when used)

and now the little rules, pls read them, they matter:

• if --samtools is skipped, samtools mpileup is called with default arguments samtools
• if --bcftools is used without parameters, samtools is called with switch -gu and bcftools is called as bcftools view -Ov
• if --bcftools is skipped, bcftools is not called

periodt 💅

💖 OPTIONS 💖

• -F, --filter=FILTER — set custom filter for alignments 🌈
• -L, --regions=FILENAME — provide BED file with regions (no need to duplicate it in samtools args); all input files must be indexed — yes, all of them, no skipping 🙈
• -o, --output-filename=<STDOUT> — specify output filename ✨
• -t, --nthreads=NTHREADS — maximum number of threads to use 🔥 go wild, but that's the ceiling
• -b, --buffer-size=4_000_000 — chunk size (in bytes) 🍓 four million bytes of chunk, as a treat

💀 BUGS 💀

ngl this section is literally empty in the original. no bugs listed, nothing, just vibes. we love a clean slate 🫶 (and fr fr, if you find one, that's a you-and-the-maintainers conversation 💜)

🌈 SEE ALSO 🌈

okay this one's on me — the original page doesn't list a SEE ALSO section, so I'm not inventing one. no fake references, we don't do that here, iykyk 💅

and that's the whole page bestie, sending you off with the cute little sign-off from the bottom of the original: this was SAMBAMBA-MILEUP(1), dated January 2015 — yeah, she's a vintage queen and she still ate 👑🦋💖