dockstore-cgpwgs

dockstore-cgpwgs provides a complete multi threaded WGS analysis for SNV, INDEL, SV and Copynumber variation with associated annotation of VCF files. This has been packaged specifically for use with the Dockstore.org framework.

Required input files are

1. Tumour BAM file
2. Normal BAM file
3. Core reference archive (e.g. core_ref_GRCh37d5.tar.gz)
4. WXS reference archive (e.g. SNV_INDEL_ref_GRCh37d5.tar.gz) ... WIP ...
5. VAGrENT (annotation) reference archive (e.g. VAGrENT_ref_GRCh37d5_ensembl_75.tar.gz)

Inputs 1&2 are expected to have been mapped using dockstore-cgpmap.

@TODO The data linked in the 'examples' area is a tiny section of chr21 from the cell line COLO-829. This will generate a small number of INDEL and SNV variants. All the SNV variants do not pass filtering (several only fail as not in a gene footprint, 'F009').

Please check the Wiki then raise an issue if you require additional information on how to generate your own reference files. Much of this information is available on the individual algorithm pages.

Release process

This project is maintained using HubFlow.

1. Make appropriate changes
2. Bump version in Dockerfile and Dockstore.cwl
3. Push changes
4. Check state on Travis
5. Generate the release (add notes to GitHub)
6. Confirm that image has been built on quay.io
7. Update the dockstore entry, see their docs.

LICENCE

Copyright (c) 2017 Genome Research Ltd.

Author: Cancer Genome Project cgpit@sanger.ac.uk

This file is part of dockstore-cgpwgs.

dockstore-cgpwgs is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see http://www.gnu.org/licenses/.

1. The usage of a range of years within a copyright statement contained within this distribution should be interpreted as being equivalent to a list of years including the first and last year specified and all consecutive years between them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007- 2009, 2011-2012’ should be interpreted as being identical to a statement that reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012’."