---
name: "subindel"
section: "1"
platform: "linux"
package: "subread"
version: "2.0.8+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/subindel"
---

# subindel(1)

toolkit for processing next-gen sequencing data

## NAME

subindel - toolkit for processing next-gen sequencing data

## DESCRIPTION

SubIndel: detect short and long indels

### Usage:

-

  subindel **-i** \<SAM file\> **-g** \<subread index\> **-o** \<output VCF\> {-d \<expected fragment distance\>} {-I \<max indel length\>} {--paired-end}

### Example:

-

  subindel **-i** my\_paired\_end\_reads.SAM **-g** my\_index **-o** my\_result **-d** 300 **-I** 200 **--paired-end**

## AUTHOR

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