Changes between Version 1 and Version 2 of GonlStart


Ignore:
Timestamp:
Jun 6, 2013 10:48:37 AM (5 years ago)
Author:
mswertz
Comment:

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  • GonlStart

    v1 v2  
    1111 * See [wiki:ComputeResources] - for information about the GoNL compute clusters
    1212 * 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 
    4813*Work organization based on regenboog project. Clearly there is much connection between all work.