[[BlogList(recent=5, max_size=250, format=float, heading=New blogs)]] = Welcome to the BBMRI/GvNL Wiki = This is the wiki for the BBMRI-NL bioinformatics and GvNL analysis working groups. * See MeetingMinutes - minutes of our Skype meetings * See ProjectOverview - description of the bioinformatics regenboog * See DataAnalysisPlan - description of the GvNL analysis objectives * See WorkPlan - description of the current planning * See ReadingMaterials - for recommended powerpoints and papers = Projects and pipelines = Work organization based on regenboog project. Clearly there is much connection between all work. See SchematicOverview. == Sequence analysis (WP1) == * SnpCallingPipeline - description of the variation analysis pipeline (UMCG?) * CoverageAnalysisPipeline - description of the coverage analysis pipeline (AMC?) * ChipBasedQcPipeline - description of the chip data comparison QC pipeline (EMC?) * MendelianQcPipeline - description of the mendelian check pipeline * DeNovoVariationPipeline - finding de novo variations in the GvNL data (LUMC?) * TrioAwareVariantDiscoveryPipeline - Trio-aware variant discovery and genotype calling pipelin == Genotype imputation (WP2) == * TrioAwarePhasingPipeline - phasing the individuals using trio informatione * ImputationPipeline - description of the imputation pipeline (VU?,UMCG?) == Catalogue and search of biobanks (WP3) == * Hackaton - hackaton in collaboration with NBIC == Genomic biobank IT infrastructure (WP4) == * DataManagement - how we use MOLGENIS to track/trace data and tools * WorkflowTools - how to configure, manage and run pipelines * BigStorage - how we store the NGS and GWAS data * BigCompute - how we will enable the pipelines on grids and clusters = Using this wiki = As all Wiki pages, this page is editable, this means that you can modify the contents of this page simply by using your web-browser. Simply click on the "Edit this page" link at the bottom of the page. WikiFormatting will give you a detailed description of available Wiki formatting commands. On top there is menu with additional features * '''Blog''' - Meetings, events etc can be blogged * '''Roadmap''' - Overview of the main objectives * '''Tickets''' - All our TODO's (per roadmap) we can collect under Tickets * '''Browse source''' - All our scripts we can browsed under Browse Source * '''Subversion''' - Programmers can commit their code using SVN at http://gbic.target.rug.nl/bbmri/svn