BamTools on Helix
BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files.
It was developed by Derek Barnett in the Marth lab at Boston College.
Programs location
/usr/local/bamtools/bin/bamtool
The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands, 'module load bamtools' , as in the example below.
Frequently used module commands:
$ module load AppName $ module load AppName/AppVersion $ module unload AppName $ module avail $ module avail AppName $ module list $ module switch AppName AppName/AppVersion $ module display AppName
If you use this application very often, in addition to use the 'module' command, you can also set the environmental variables in your /home/UserID/.bashrc or /home/userID/.cshrc file so that it will be done automatically when you login and you don't need to set the environmental variable(s) everytime.
For bash users:
$ export PATH=/usr/local/bamtools-2.2.0/bin:$PATH $ export LD_LIBRARY_PATH=/usr/local/bamtools-2.2.0/lib/:$LD_LIBRARY_PATH
For tcsh/csh users:
% set path=(/usr/local/bamtools-2.2.0/bin ${path})
% setenv LD_LIBRARY_PATH /usr/local/bamtools-2.2.0/lib:$LD_LIBRARY_PATH
How To Use
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) | |
| sort | Sorts the BAM file according to some criteria | |
| split | Splits a BAM file on user-specifed 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.
Example:
$ module load bamtools
$ bamtools filter -in data1.bam -in data2.bam -mapQuality ">50" | bamtools count
This will give a count of all alignments in your 2 BAM files with a mapQuality of greater than 50. And any tool writing to stdout can be piped into other utilities.
