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