---
name: "svim"
section: "1"
platform: "linux"
package: "svim"
version: "2.0.0-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/svim"
---

# svim(1)

Structural variant caller for long sequencing reads

## NAME

svim - Structural variant caller for long sequencing reads

## DESCRIPTION

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

SVIM (pronounced SWIM) is a structural variant caller for long reads. It discriminates six different variant classes: deletions, tandem and interspersed duplications, inversions, insertions and translocations. SVIM is unique in its capability of extracting both the genomic origin and destination of duplications.

SVIM consists of four major steps: - COLLECT detects signatures for SVs in long read alignments - CLUSTER merges signatures that come from the same SV - COMBINE combines clusters from different genomic regions and classifies them into distinct SV types - GENOTYPE uses alignments spanning SVs to determine their genotype

SVIM can process two types of input. Firstly, it can detect SVs from raw reads by aligning them to a given reference genome first ("SVIM.py reads \[options\] working\_dir reads genome"). Alternatively, it can detect SVs from existing reads alignments in SAM/BAM format ("SVIM.py alignment \[options\] working\_dir bam\_file").

### positional arguments:

- {reads,alignment}

  modes

- reads

  Detect SVs from raw reads. Align reads to given reference genome first.

- alignment

  Detect SVs from an existing alignment

### optional arguments:

- **-h**, **--help**

  show this help message and exit

- **--version**, **-v**

  show program's version number and exit

## AUTHOR

 This manpage was written by Nilesh Patra for the Debian distribution and\
  can be used for any other usage of the program.