[[BlogList(recent=5, max_size=250, format=float, heading=New blogs)]] = BBMRI-NL Rainbow projects: = * [GonlStart RP2 - Dynamic bioinformatics infrastructures for biobank enrichment] * [FgStart RP3 - Functional genomics] To gain access to restricted areas please * email m.a.swertz AT rug.nl or pieter.neerincx AT gmail.com (for RP2) * patrickdeelen AT gmail.com or M.H.Moed AT lumc.nl (for RP3) = SOPs and Pipelines: = * '''Sequence analysis''' * 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) * StructuralVariationPipeline - finding indels/inversions/CNV/translocations in the GvNL data (SV group) * 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''' * [wiki:Imputations] - Work group main page * [wiki:PhenotypeAnalysis] - Work group main page * 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) * [http://www.bbmriwiki.nl/wiki/Impute2Pipeline Impute2Pipeline] - description of the Impute2 pipeline (UMCG) * AlleleCounting - count alleles accross a set of sample.vcf * '''Catalogue and search of biobanks''' * [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''' * 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) = 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 projects are developed in collaboration with = [[Image(bbmri.gif)]] [[Image(nbic.png)]]