| | 1 | = Dynamic bioinformatics infrastructures for biobank enrichment (BBMRI-NL rainbow 2)= |
| | 2 | This 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. |
