SVIM(1)

💖 SVIM(1) — the structural variant caller that ate 💖

okay bestie, sit down, hydrate, and let me tell you about svim, which lives in section 1 of the manual (user commands, obviously, it's a whole program) ✨

🌸 NAME 🌸

svim — a structural variant caller for long sequencing reads. yes. long reads. the main character of sequencing data 💅

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🦋 SYNOPSIS 🦋

usage: svim [-h] [--version] {reads,alignment} ...

like, that's the whole shape of it. pick a mode, or ask for help, or ask for the version. that's the vibe check 🎀

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💜 DESCRIPTION 💜

SVIM — and yes, you pronounce it like "SWIM", not "ess-vim", I will not be taking questions — is a structural variant caller for long reads. it's out here discriminating between six different variant classes, no cap:

• deletions
• tandem duplications
• interspersed duplications
• inversions
• insertions
• translocations

and here's the part where SVIM is genuinely unique, like it's not even a competition: it can extract both the genomic origin and the genomic destination of duplications. both. origin AND destination. the way that it does that… obsessed 😭👑

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✨ the four major steps ✨ (the pipeline, the journey, the character arc)

1. COLLECT — detects signatures for SVs in long read alignments 🕵️
2. CLUSTER — merges signatures that come from the same SV 🫂
3. COMBINE — combines clusters from different genomic regions and classifies them into distinct SV types 🧩
4. GENOTYPE — uses alignments spanning SVs to determine their genotype 🧬

four steps. iconic behaviour. periodt.

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🌈 the two ways to feed it 🌈

SVIM can process two types of input, bestie, so pick your fighter:

• first up: it can detect SVs from raw reads by aligning them to a given reference genome first:

SVIM.py reads [options] working_dir reads genome

• or alternatively: it can detect SVs from existing read alignments in SAM/BAM format:

SVIM.py alignment [options] working_dir bam_file

both are valid. both are slay. choose based on what you already have lying around 💖

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🌸 positional arguments 🌸

• {reads,alignment} — these are the modes. the fork in the road. the two doors. choose one, you can't have both 🙈
• reads — Detect SVs from raw reads. Align reads to given reference genome first. (yes, it does the aligning for you first, it's giving generous ✨)
• alignment — Detect SVs from an existing alignment. (you already did the aligning, so it just gets straight to the point 💅)

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🎀 optional arguments 🎀

• -h, --help — show this help message and exit. the classic. the comfort blanket. when in doubt, -h 🫶
• --version, -v — show program's version number and exit. very demure, very mindful, tells you what version you're on 🌟

fr fr though — if you're ever lost, just hit -h. it will never judge you. it's literally there for that 💜

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👑 AUTHOR 👑

This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program. ty for your service Nilesh, we appreciate you 🫡🌸

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🌈 SEE ALSO 🌈

okay so there aren't any SEE ALSO entries in this one, bestie — that's the whole page. no cross-references, no extra reading, we keep it self-contained. a minimalist queen 💅

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psst, bestie: remember that this is svim version 2.0.0, dated July 2021 — so if you're running something wildly different, don't come for me, come for the version number 💀✨

and that's the whole page! go call some structural variants, you absolute icon 🦋💖