BAMStats is a tool for extracting coverage, and other data, from BAM format mapping files, and generating descriptive statistics of that data.

1. Installation
Unpack zip archive to a convenient location. Zip archive contains two executables and a lib directory containing third-party jar files used by BAMStats. Ensure lib directory remains with executables.

2. Running BAMstats
To run BAMStats, use the following command (in this example 4GB is allocated with the -Xmx flag):
java -jar -Xmx4g BAMStats-GUI-1.25.jar

To run the command-line version of BAMStats use the following command:
java -jar -Xmx4g BAMStats-1.25.jar -i <BAM file>

For a full list of command line options: java -jar BAMStats-1.20.jar -h

Notes
1. BAMStats typically requires 2 to 6 GB of computer memory allocated to it (as a Java program, this is achieved with the -Xmx flag when running the program from the command line).
2. BAMStats will except either SAM or BAM formatted files but these must be sorted.

Requirements:
* Java

The license of this software is Free, you can free download and free use this calculator software.