---
name: "bamtools"
section: "1"
platform: "linux"
package: "bamtools"
version: "2.5.2+dfsg-6+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bamtools"
---

# bamtools(1)

toolkit for manipulating BAM (genome alignment) files

## NAME

bamtools - toolkit for manipulating BAM (genome alignment) files

## SYNOPSIS

**bamtools** \[--help\] COMMAND \[ARGS\]

## DESCRIPTION

BamTools facilitates research analysis and data management using BAM files.  It copes with the enormous amount of data produced by current sequencing technologies that is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research.

## OPTIONS

- convert

  Converts between BAM and a number of other formats

- count

  Prints number of alignments in BAM file(s)

- coverage

  Prints coverage statistics from the input BAM file

- filter

  Filters BAM file(s) by user-specified criteria

- header

  Prints BAM header information

- index

  Generates index for BAM file

- merge

  Merge multiple BAM files into single file

- random

  Select random alignments from existing BAM file(s), intended more as a testing tool.

- resolve

  Resolves paired-end reads (marking the IsProperPair flag as needed)

- revert

  Removes duplicate marks and restores original base qualities

- sort

  Sorts the BAM file according to some criteria

- split

  Splits a BAM file on user-specified property, creating a new BAM output file for each value found

- stats

  Prints some basic statistics from input BAM file(s)

See 'bamtools help COMMAND' for more information on a specific command.