[[BlogList(recent=5, max_size=250, format=float, heading=New blogs)]] = Welcome to the BBMRI/GvNL 'bionformatics for biobanking' wiki = This is the wiki for the [http://www.bbmri.nl BBMRI-NL bioinformatics and GvNL analysis working groups] in collaboration with the [http://www.nbic.nl NBIC] [https://wiki.nbic.nl/index.php/Biobanking Biobanking task force] and [https://wiki.nbic.nl/index.php/Next_Generation_Sequencing NBIC sequencing task force] * 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 * See DataManagement - for Data Management strategy * See [wiki:BGIDatasets] - for information about BGI data * See [wiki:Clusters] - for information about the GoNL compute clusters * Join our [https://trac.nbic.nl/mailman/listinfo/biobanking-interest mailing list] = Projects and pipelines: = * '''Sequence analysis (WP1)''' * SchematicOverview - overview of the pipelines needed * SnpCallingPipeline - description of the variation analysis pipeline (UMCG) * DataConcordance - comparison of sequence data vs genotype chip data (UMCG) * CoverageAnalysisPipeline - description of the coverage analysis pipeline (AMC) * GwasQcPipeline - description of immunochip QC before ngs-chip comparison (UMCG) * ChipBasedQcPipeline - description of the chip data comparison QC pipeline (EMC) * MendelianQcPipeline - description of the mendelian check pipeline (EMC) * DeNovoVariationPipeline - finding de novo variations in the GvNL data (LUMC) * TrioAwareVariantDiscoveryPipeline - Trio-aware variant discovery and genotype calling pipeline (UU) * GenomeViewer - view read and snp data in their genomic context, e.g. using IGV * [http://www.molgenis.org/wiki/NgsWorkbench Next Generation Sequence LIMS] - track and trace all GoNL samples and analysis (UMCG) * SequencingIntersection - Find shared variants among samples (UMCG) * '''Genotype analysis and imputation (WP2)''' * TrioAwarePhasingPipeline - phasing the individuals using trio information (EMC) * SnpAnnotationPipeline - annotating SNPs with known functional information (LUMC,UMCG) * ImputationPipeline - description of the imputation pipeline (VU,UMCG) * '''Catalogue and search of biobanks (WP3)''' * [http://www.phenoflow.org/wiki/BiobankCatalog Catalog of Dutch biobanks] - in collaboration with [https://wiki.nbic.nl/index.php/Biobanking NBIC biobanking task force] * [https://sites.google.com/a/nbiceng.net/hackathonii Connecting biobanks Hackaton] - in collaboration with [https://wiki.nbic.nl/index.php/Interoperability NBIC interoperability task force] * '''Genomic biobank IT infrastructure (WP4)''' * DataManagement - how we use MOLGENIS to track/trace data and tools (UMCG) * WorkflowTools - how to configure, manage and run pipelines (UMCG,AMC) * SequenceBIMS - to have report on samples, raw/intermediate/result data and processing pipelines run * GwasBIMS - to have report on samples, imputation runs and results * ApplyForDataTool - to provide researchers with a way to request access to BBMRI-NL data sets * BigStorage - how we store the NGS and GWAS data (UMCG,SARA,CIT) * BigCompute - how we will enable the pipelines on grids and clusters (UMCG,AMC,SARA,CIT) *Work organization based on regenboog project. Clearly there is much connection between all work. = 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 = BBMRI bioinformatics and genome of the netherlands project are developed in collaboration with = [[Image(bbmri.gif)]] [[Image(nbic.png)]]