Bam2Wig is a small pipeline consisting of three steps that is used to convert BAM files into track coverage files: bigWig, wiggle, and TDF. While this seems like a task that should be tool, at the time of writing, there are no command line tools that can do such conversion in one go. Thus, the Bam2Wig pipeline was written.


The required configuration file for Bam2Wig is really minimal, only a single JSON file containing an output_dir entry:

{"output_dir": "/path/to/output/dir"}

Running Bam2Wig

As with other pipelines, you can run the Bam2Wig pipeline by invoking the pipeline subcommand. There is also a general help available which can be invoked using the -h flag:

$ java -jar /path/to/biopet.jar pipeline sage -h

If you are on SHARK, you can also load the biopet module and execute biopet pipeline instead:

$ module load biopet/v0.3.0
$ biopet pipeline bam2wig

To run the pipeline:

 biopet pipeline bam2wig -config </path/to/config.json> -qsub -jobParaEnv BWA -run

Output Files

The pipeline generates three output track files: a bigWig file, a wiggle file, and a TDF file.