[[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)]]