bamtools

Version:: 2.5.2
Category:: bio
Cluster:: Loki

Author / Distributor

https://github.com/pezmaster31/bamtools/

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.

Documentation

usage: bamtools [--help] COMMAND [ARGS]

Available bamtools commands:
      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)

Examples/Usage

List available modules:
```
$ module avail bamtools
```
Load the Anaconda module:
```
$ module load bio/bamtools/2.5.2
```
Check the loaded modules:
```
$ module list
```
Unload the Anaconda module:
```
$ module unload bio/bamtools/2.5.2
```
Converts between BAM and a number of other formats:
```
$ bamtools convert
```
Generates index for BAM file:
```
$ bamtools index
```

Installation

Source code is obtained from Bamtools