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ICGC PanCanQC Docker

This is the first version of the Docker to calculate the quality control values used in the ICGC PanCan project.

Installation

First of all you need to have a running Docker installation.

Then clone this repository.

$ cd PanCanQC/
$ docker build -t "pcawg-qc" .

Running the Docker

Then just run the Docker:

$ docker run \
		-v /path/to/your/tumor.bam:/home/pcawg/data/bams/tumor.bam \
		-v /path/to/your/control.bam:/home/pcawg/data/bams/control.bam \
		-v /path/to/results_dir/:/home/pcawg/data/results/ \
		-t pcawg-qc

You should fine a file with the results in the /path/to/results_dir/ directory.