IntOGen - Pipeline

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• dc.contributor.author González-Pérez, Abelca
• dc.contributor.author Pérez Llamas, Christian, 1976-ca
• dc.contributor.author Tamborero Noguera, Davidca
• dc.contributor.author Schroeder, Michael Philipp, 1986-ca
• dc.contributor.author Jené i Sanz, Alba, 1984-ca
• dc.contributor.author Santos, Albertoca
• dc.contributor.author López Bigas, Núriaca
• dc.contributor.author Déu Pons, Jordica
• dc.date.accessioned 2016-12-21T11:51:09Z
• dc.date.available 2016-12-21T11:51:09Z
• dc.date.issued 2016-07-18
• dc.description Requirements: IntOGen depends on **Python 3.4** or above and some python libraries. If you don't have Python 3.4 already installed, the easiest way to install all this software stack is using the well known [Anaconda Python distribution](http://continuum.io/downloads#34). /nAlso **Perl 5.10** (with DBI module installed) or above has to be available at PATH to be able to run VEP scripts./n By default MutsigCV is disabled. If you want to enable it you have to first download and install [Matlab Runtime](http://es.mathworks.com/products/compiler/mcr/) and MutsigCV](https://www.broadinstitute.org/cancer/cga/mutsig) and then edit the IntOGen configuration file that by default it's at /.intogen/system.conf (parameters: mutsig_enabled, mutsig_path and matlab_mcr) /nInstallation: To install or update to the last stable version of IntOGen you need to run: /n $ pip install intogen pandas=0.17/nAfter this you will have the `intogen` script available at your path and if this is the first time that you install IntOGen you need to run the setup to download all the data dependencies. This setup will download 3.6Gb of data that after uncompress it will need 9Gb of free space. /n $ intogen --setup/n**TIP**: By default the IntOGen configuration files are in `/.intogen` if you want to change this folder you need to define/nthe system environment variable **INTOGEN_HOME** using the `export` command. Also, all the datasets are downloaded by/ndefault at `/.bgdata` if you want to change this folder you need to define the system environment variable **BGDATA_LOCAL**./nRun an example:/nDownload and extract some samples VCF files:/n $ wget https://bitbucket.org/intogen/intogen-pipeline/downloads/intogen-samples.tar.gz/n $ tar xvzf intogen-samples.tar.gz /nRun IntOGen using the default tasks configuration./n $ intogen -i sample1.vcf -i sample2.vcf -i sample3.vcf -i sample4.vcf /nBrowse the results at the `output` folder./n /nCustom configuration:/nAt `/.intogen/task.conf` you can check the default task configuration values. If you want to run the pipeline /nusing different parameters you can change the default values or create a `.smconfig` file for each project. /nThe `.smconfig` files are a copy of `/.intogen/task.conf` but adding `id` and `files` parameters. The `id` is the name /nof the project and the `files` is a list separated by comma of all the files (MAF, VCF or tab format) that contain /nsamples for that project. /nYou can create a `.smconfig` file like this:/n $ echo -e "id = allsamples/nfiles = sample1.vcf,sample2.vcf,sample3.vcf,sample4.vcf/n" > allsamples.smconfig/n $ cat /.intogen/task.conf >> allsamples.smconfig/nTo run it again, you need to delete or move the previous output and run using the `.smconfig` file as input./n $ rm -rf output/n $ intogen -i allsamples.smconfig /nIf you want to run multiple projects at once you can create multiple `.smconfig` files in one folder and then give that/nfolder as input.ca
• dc.description.abstract Analyses somatic mutations in thousands of tumor genomes to identify cancer driver genes.ca
• dc.identifier.doi https://doi.org/10.34810/data407
• dc.identifier.uri http://hdl.handle.net/10230/27810
• dc.language.iso engca
• dc.publisher Universitat Pompeu Fabraca
• dc.relation Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Tamborero D, Schroeder MP, Jene-Sanz A, Santos A, Lopez-Bigas N. IntOGen-mutations identifies cancer drivers across tumor types. Nat Methods. 2013; 10 (11): 1081-2. DOI: 10.1038/nmeth.2642
• dc.relation Més informació: IntOGen pipeline (Bitbucket)
• dc.relation.isreferencedby http://dx.doi.org/10.1038/nmeth.2642
• dc.relation.uri https://bitbucket.org/intogen/intogen-pipeline
• dc.rights IntOGen Mutations Analysis is the property of the Universitat Pompeu Fabra (UPF), which hold the copyright thereto. Copyright® 2012-2014 Universitat Pompeu Fabra./nIntOGen Mutations Analysis is made available to the general public subject to certain conditions described in its license. For the avoidance of doubt, you may use the software and any data accessed through UPF software for academic, non-commercial and personal use only, and you may not copy, distribute, transmit, duplicate, reduce or alter in any way for commercial purposes, or for the purpose of redistribution, without a license from the Universitat Pompeu Fabra (UPF). Requests for information regarding a license for commercial use or redistribution of IntOGen Mutations Analysis may be sent via e-mail to innovacio@upf.edu./nThird Party Software - Third Party Data/nThe following software may be included in the code and, unless otherwise specified, is licensed under the licenses described below. The disclaimers and copyright notices provided are based on information made available to UPF by the third party licensors listed:/n- VEP/n- Ensembl/n- LiftOver/nRegarding third-party data, you agree to comply with the terms and conditions described in the licenses provided below, based on information made available to UPF by the third party licensors listed:/n- Ensembl genes: www.ensembl.org European Bioinformatic Institute./n- Mutation assessor 2: www.mutationassessor.org Computational Biology Center/n- Memorial Sloan Kettering Cancer Center./n- KEGG: http://www.genome.jp/kegg//n- Gene Ontology: http://www.geneontology.org//n- ICGC: http://icgc.org//n- TCGA: http://cancergenome.nih.gov//nAll rights in any third-party data and/or any third-party software, including all ownership rights, are reserved and remain with the respective third parties. You agree that these third parties may enforce their rights under this agreement against you directly in their own name.ca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.rights.uri http://bg.upf.edu/licenses/intogen-mutations-analysis-license.txtca
• dc.subject.keyword Cancer genesen
• dc.subject.keyword Canceren
• dc.subject.keyword Mutation analysisen
• dc.subject.keyword Gene driveen
• dc.title IntOGen - Pipelineca
• dc.type info:eu-repo/semantics/otherca
• dc.type Software