Dynamic bioinformatics infrastructures for biobank enrichment (BBMRI-NL rainbow 2)

This is the wiki for the Dynamic bioinformatics infrastructures for biobank enrichment project of ​BBMRI-NL (rainbow project 2) in collaboration with the Genome of the Netherlands project (​GoNL, BBMRI-NL rainbow project 1), UMCG, UMCU, VU, ErasmusMC, LUMC and NBIC.

• See MeetingMinutes - minutes of our Skype meetings (members only)
• 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 BGIDatasets - for information about BGI data
• See ComputeResources - for information about the GoNL compute clusters
• Join our ​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)
  • 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
  • ​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)
  • Imputations - Work group main page
  • 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)
  • Impute2Pipeline - description of the Impute2 pipeline (UMCG)
  • AlleleCounting - count alleles accross a set of sample.vcf
• Catalogue and search of biobanks (WP3)
  • ​Catalog of Dutch biobanks - in collaboration with ​NBIC biobanking task force
  • ​Connecting biobanks Hackaton - in collaboration with ​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.