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A Quality Control application for BAM files

BamQC is an application which takes a BAM file containing mapped data and runs a series of tests on it to generate a comprehensive QC report. This will help you to understand your data and will tell you if there is anything unusual the files you have analysed. Each test is flagged as a pass, warning or fail depending on how far it departs from what you'd expect from a normal large data set with no significant biases.

It's important to stress that warnings or even failures do not necessarily mean that there is a problem with your data, only that it is unusual. It is possible that the biological nature of your sample means that you would expect this particular bias in your results.

Interactive Graphical or Command Line

BamQC can be run either as an interactive graphical application which allows you to view results for multiple files in a single application. Alternatively you can run the program in a non interactive way (say as part of a pipeline) which will generate an HTML report for each file you process.

Cross-platform Java

BamQC is a cross-platform application, written in java. In theory it should run on any platform which has a suitable java runtime environment. It is been tested on Windows, MacOSX 10.6 and Linux running Java v1.6, v1.7 and v1.8.

##Download Check out of GitHub and using git:

git clone


To compile the source code of BamQC, a Java Compiler (JDK v1.6, v1.7, v1.8, and the package Ant ( are required. The correct installation of these two packages can be tested by typing the commands:

# Test for the Java Compiler 
javac -version
# Example of output: 
# > javac 1.7.0_85

# Test for Ant
# Example of output if no build.xml is located in the same folder
# > Buildfile: build.xml does not exist!
# > Build failed

BamQC can be easily built using the following commands:

# Move to the folder of BamQC
cd Path/To/BamQC/SourceCode/

# Type the command "ant". This will automatically process 
# the BamQC file build.xml 

# Move to the bin folder which was created in the previous step.
cd bin

# Change permission to the file bamqc in order to execute it
chmod 755 bamqc

# Test 


Further instructions for installing and running the program can be found in the installation instructions file in the BamQC distribution.


If you have any comments about BamQC we would like to hear them. You can either enter them as a new issue on github.

Or email them directly to: simon.andrews at


Mapped QC analysis program



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