BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
- Puhti: 2.5.1
- Chipster graphical user interface
In Puhti, Bamtools can be taken in use as a part of biokit module collection:
module load biokit
The biokit modules sets up a set of commonly used bioinformatics tools. Note however that there are bioinformatics tools in Puhti, that have a separate setup commands.
The syntax of bamtools is:
bamtools COMMAND ARGUMENTS
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)
For more information on a specific command, run command:
bamtools help COMMAND
More information about Bamtoos can be found from the Bamtools home page.