Changes between Initial Version and Version 1 of GonlStart


Ignore:
Timestamp:
Jun 6, 2013 10:44:49 AM (8 years ago)
Author:
Morris Swertz
Comment:

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  • GonlStart

    v1 v1  
     1= Dynamic bioinformatics infrastructures for biobank enrichment (BBMRI-NL rainbow 2)=
     2This is the wiki for the Dynamic bioinformatics infrastructures for biobank enrichment project of [http://www.bbmri.nl BBMRI-NL (rainbow project 2)] in collaboration with the Genome of the Netherlands project ([http://www.nlgenome.nl GoNL], BBMRI-NL rainbow project 1), UMCG, UMCU, VU, ErasmusMC, LUMC and NBIC.
     3
     4 * See MeetingMinutes - minutes of our Skype meetings (members only)
     5 * See ProjectOverview - description of the bioinformatics regenboog
     6 * See DataAnalysisPlan - description of the GvNL analysis objectives
     7 * See WorkPlan - description of the current planning
     8 * See ReadingMaterials - for recommended powerpoints and papers
     9 * See DataManagement - for Data Management strategy
     10 * See [wiki:BGIDatasets] - for information about BGI data
     11 * See [wiki:ComputeResources] - for information about the GoNL compute clusters
     12 * Join our [https://trac.nbic.nl/mailman/listinfo/biobanking-interest mailing list]
     13= Projects and pipelines: =
     14 * '''Sequence analysis (WP1)'''
     15   * SchematicOverview - overview of the pipelines needed
     16   * SnpCallingPipeline - description of the variation analysis pipeline (UMCG)
     17   * DataConcordance - comparison of sequence data vs genotype chip data (UMCG)
     18   * CoverageAnalysisPipeline - description of the coverage analysis pipeline (AMC)
     19   * GwasQcPipeline - description of immunochip QC before ngs-chip comparison (UMCG)
     20   * ChipBasedQcPipeline - description of the chip data comparison QC pipeline (EMC)
     21   * MendelianQcPipeline - description of the mendelian check pipeline (EMC)
     22   * DeNovoVariationPipeline - finding de novo variations in the GvNL data (LUMC)
     23   * StructuralVariationPipeline - finding indels/inversions/CNV/translocations in the GvNL data (SV group)
     24   * TrioAwareVariantDiscoveryPipeline - Trio-aware variant discovery and genotype calling pipeline (UU)
     25   * GenomeViewer - view read and snp data in their genomic context, e.g. using IGV
     26   * [http://www.molgenis.org/wiki/NgsWorkbench Next Generation Sequence LIMS] - track and trace all GoNL samples and analysis (UMCG)
     27   * SequencingIntersection - Find shared variants among samples (UMCG)
     28 * '''Genotype analysis and imputation (WP2)'''
     29   * [wiki:Imputations] - Work group main page
     30   * [wiki:PhenotypeAnalysis] - Work group main page
     31   * TrioAwarePhasingPipeline - phasing the individuals using trio information (EMC)
     32   * SnpAnnotationPipeline - annotating SNPs with known functional information (LUMC,UMCG)
     33   * ImputationPipeline - description of the imputation pipeline (VU,UMCG)
     34   * [http://www.bbmriwiki.nl/wiki/Impute2Pipeline Impute2Pipeline] - description of the Impute2 pipeline (UMCG)
     35   * AlleleCounting - count alleles accross a set of sample.vcf
     36 * '''Catalogue and search of biobanks (WP3)'''
     37   * [http://www.phenoflow.org/wiki/BiobankCatalog Catalog of Dutch biobanks] - in collaboration with [https://wiki.nbic.nl/index.php/Biobanking NBIC biobanking task force]
     38   * [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]
     39 * '''Genomic biobank IT infrastructure (WP4)'''
     40   * DataManagement - how we use MOLGENIS to track/trace data and tools (UMCG)
     41   * WorkflowTools - how to configure, manage and run pipelines (UMCG,AMC)
     42   * SequenceBIMS - to have report on samples, raw/intermediate/result data and processing pipelines run
     43   * GwasBIMS - to have report on samples, imputation runs and results
     44   * ApplyForDataTool - to provide researchers with a way to request access to BBMRI-NL data sets
     45   * BigStorage - how we store the NGS and GWAS data (UMCG,SARA,CIT)
     46   * BigCompute - how we will enable the pipelines on grids and clusters (UMCG,AMC,SARA,CIT)
     47
     48*Work organization based on regenboog project. Clearly there is much connection between all work.