DNAp WES/WGS Pipeline

Docker Image Bundle

The following link will allow you to download an archived version of the Docker image bundle containing the pipeline.

This is a large download (~1.6GB).

The .tar.gz file you will download should be extracted to produce a directory containing setup instructions and a helper script for running the pipeline container in Docker, as well as the image archive itself (also a .tar.gz file).

Download link: (version from "DNAp: A Pipeline for DNA-seq Data Analysis") dna-pipeline-bundle_20171219.tar.gz (Version 12/19/2017, Updated 03/21/2018)

Download link: (version with BWA-0.7.17 (r1188)) dna-pipeline-bundle_20180311.tar.gz (Version 03/11/2018, Updated 03/21/2018)

Example Directories

The archives linked below are for an example of the suggested working and reference directory structures for the pipeline. The reference directory archive contains all necessary files for the hg19 human genome build. There are example .bed files for WES intervals included as well, but you will need to add the correct .bed file corresponding to your actual WES library kit, and configure the pipeline to use that file (see documentation).

Example working directory (just creates the folder structure for you).
Download link: pipeline_example_workingdir.tar.gz (Updated 06/30/2016)

Example Reference directory with COSMIC version 77 update included.
If you already have the reference directory set up, just download the "cosmic_v77.tar.gz" archive below (see instructions there).
NOTE: This is a very large download (~20GB) due to the included Oncotator database.
Download link: pipeline_example_referencedir_COSMIC_v77.tar.gz (Updated 07/31/2016)

COSMIC Version 77 update for the legacy version of the Reference directory. Extract this archive and move the two files "hg19_CosmicCombinedMuts_v77.vcf" and "hg19_CosmicCombinedMuts_v77.vcf.idx" ito the "hg19" subdirectory of your existing reference directory. As of the July release the pipeline's default configuration will look for these files there. (You can modify this in the WES_ or WGS_config.groovy configuration files.)
Download link:cosmic_v77.tar.gz (Updated 07/31/2016)

The following link contains the necessary files for running on mouse (Mus musculus) data. You should extract it inside the reference data directory created by the archive above, or see the documentation for the correct directory layout if you are doing something custom. The Snpeff database is not included, but it will automatically be downloaded when required.
NOTE: This is a large download (~5.5GB).
Download link: mouse_GRCm38.tar.gz (Updated 06/30/2016)

Utility

The following utility Bash script will shut down your Google Compute Engine VM as soon as it detects that Bpipe (running in the pipeline container) has exited. To make use of this, you should start a tmux or screen session (or login to the VM with two sessions). Start the pipeline in one session and then run this script in the other session. You can then detach from the VM and it will be shut down automatically when Bpipe exits.
Download link:shutdown_after_bpipe.sh (Updated 07/31/2016)

Documentation

Download link: pipeline_documentation.pdf (Updated 06/30/2016)

Supplemental Information for "DNAp: A Pipeline for DNA-seq Data Analysis"

Supplemental information for the paper "DNAp: A Pipeline for DNA-seq Data Analysis" is available by downloading the ZIP archive linked below:

Download link: DNAp_A_Pipeline_for_DNA-seq_Data_Analysis__supplemental.zip