BamTools
From HPC users
Introduction
BamTools provides a small, but powerful suite of command-line utility programs for manipulating and querying BAM files for data.
Available bamtools commands are:
- 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)
| command | description |
|---|---|
| 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 |
Installed version
The currently installed version is 2.4.0.
Using BamTools with the HPC Cluster
If you want to find out more about BEDtools on the HPC Cluster, you can use the command
module spider bamtools
This will show you basic informations e.g. a short description and the currently installed version.
To load the desired version of the module, use the command
module load BamTools/2.4.0-intel-2016b
Always remember: this command is case sensitive!
After loading the module, you can use the program with
bamtools <COMMAND> [ARGS]
Documentation
Further Information can be found on the project website.
