Copyright (c) 2015 Genome Research Ltd.

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

This file is part of TraFiC.

TraFiC 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'."

TraFiC (Transposon Finder in Cancer) uses paired-end sequencing data for the identification of somatic insertion of transposable elements. The identification of somatic TEs is performed in four steps:

1. Selection of candidate reads.
2. Transposable element masking.
3. Clustering and prediction of insertions sites.
4. Filtering of germline events.

The final results are found in the filtered.txt file. Columns are defined as follows:

• CHR - Chromosome of somatic insertion
• FAMILY - Transposon type
• P_L_POS - Left position of positive cluster supporting somatic insertion
• P_R_POS - Right position of positive cluster supporting somatic insertion
• P_TOTAL_READS - Total number of reads supporting somatic insertion in positive cluster
• P_SINGLE_END_COUNT - Number of Single-end reads supporting somatic insertion in positive cluster
• P_INTER_CHROM_COUNT - Number of Inter-chromosomal reads supporting somatic insertion in positive cluster
• P_ABERRANT_COUNT - Number of Intra-chromosomal reads supporting somatic insertion in positive cluster
• P_SINGLE_END_READS - Names of Single-end reads supporting somatic insertion in positive cluster
• P_INTER_CHROM_READS - Names of Inter-chromosomal reads supporting somatic insertion in positive cluster
• P_ABERRANT_READS - Names of Intra-chromosomal reads supporting somatic insertion in positive cluster
• N_L_POS - Left position of negative cluster supporting somatic insertion
• N_R_POS - Right position of negative cluster supporting somatic insertion
• N_TOTAL_READS - Total number of reads supporting somatic insertion in negative cluster
• N_SINGLE_END_COUNT - Number of Single-end reads supporting somatic insertion in negative cluster
• N_INTER_CHROM_COUNT - Number of Inter-chromosomal reads supporting somatic insertion in negative cluster
• N_ABERRANT_COUNT - Number of Intra-chromosomal reads supporting somatic insertion in negative cluster
• N_SINGLE_END_READS - Names of Single-end reads supporting somatic insertion in negative cluster
• N_INTER_CHROM_READS - Names of Inter-chromosomal reads supporting somatic insertion in negative cluster
• N_ABERRANT_READS - Names of Intra-chromosomal reads supporting somatic insertion in negative cluster

Events supported by at minimum of 5 reads in the both the positive and negative clusters are considered highly accurate.

###Dependencies/Install

Please install the following first:

• PCAP-core
• RepeatMasker
  • We recommend the RMBlast engine as it is easy to obtain (crossmatch is slightly faster)

Please see these for any child dependencies.

Once complete please run:

./setup.sh /some/install/location

This installs Bedtools and the TraFiC codebase.

##Creating a release ####Preparation

• Commit/push all relevant changes.
• Pull a clean version of the repo and use this for the following steps.

####Cutting the release This should be carried out using hubflow tools

1. Update perl/lib/Sanger/CGP/TraFiC.pm to the correct version.
2. Update Changes to show major items.
3. Run ./prerelease.sh
4. Check all tests and coverage reports are acceptable.
5. Commit the updated docs tree and updated module/version.
6. Push commits.
7. Use the GitHub tools to add details to the generated tag.
8. Add relevant *.tar.gz for reference data to release.