---
name: "NanoSV"
section: "1"
platform: "linux"
package: "nanosv"
version: "1.2.4+git20190409.c1ae30c-7"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/NanoSV"
---

# NanoSV(1)

structural variant caller for the Nanopore

## NAME

NanoSV - structural variant caller for the Nanopore

## DESCRIPTION

usage: NanoSV \[-h\] \[-t THREADS\] \[-s SAMBAMBA\] \[-c CONFIG\] \[-b BED\] \[-o OUTPUT\]

-

  \[-f SNP\_FILE\] \[-v\] bam

Put here a description.

### positional arguments:

- bam

  */path/to/file.bam*

### options:

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

  show this help message and exit

- **-t** THREADS, **--threads** THREADS

  Number of threads \[default: 4\]

- **-s** SAMBAMBA, **--sambamba** SAMBAMBA

  Give the full path to the sambamba or samtools executable \[default: sambamba \]

- **-c** CONFIG, **--config** CONFIG

  Give the full path to your own ini file \[ default: config.ini \]

- **-b** BED, **--bed** BED

  Give the full path to your own bed file, used for coverage depth calculations \[default: human\_hg19.bed \]

- **-o** OUTPUT, **--output** OUTPUT

  Give the full path to the output vcf file \[default: \<stdout\> \]

- **-f** SNP\_FILE, **--snp\_file** SNP\_FILE

  Give full path to the SNP variant file for phasing. Supporting file formats: BED and VCF

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

  show program's version number and exit

## SEE ALSO

The full documentation for **NanoSV** is maintained as a Texinfo manual.  If the **info** and **NanoSV** programs are properly installed at your site, the command

-

  **info NanoSV**

should give you access to the complete manual.