Changes between Version 70 and Version 71 of WikiStart


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Timestamp:
Jun 6, 2013 10:49:14 AM (6 years ago)
Author:
mswertz
Comment:

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  • WikiStart

    v70 v71  
    66* [FgStart RP3 - Functional genomics]
    77
     8
     9= Projects and pipelines: =
     10 * '''Sequence analysis'''
     11   * SchematicOverview - overview of the pipelines needed
     12   * SnpCallingPipeline - description of the variation analysis pipeline (UMCG)
     13   * DataConcordance - comparison of sequence data vs genotype chip data (UMCG)
     14   * CoverageAnalysisPipeline - description of the coverage analysis pipeline (AMC)
     15   * GwasQcPipeline - description of immunochip QC before ngs-chip comparison (UMCG)
     16   * ChipBasedQcPipeline - description of the chip data comparison QC pipeline (EMC)
     17   * MendelianQcPipeline - description of the mendelian check pipeline (EMC)
     18   * DeNovoVariationPipeline - finding de novo variations in the GvNL data (LUMC)
     19   * StructuralVariationPipeline - finding indels/inversions/CNV/translocations in the GvNL data (SV group)
     20   * TrioAwareVariantDiscoveryPipeline - Trio-aware variant discovery and genotype calling pipeline (UU)
     21   * GenomeViewer - view read and snp data in their genomic context, e.g. using IGV
     22   * [http://www.molgenis.org/wiki/NgsWorkbench Next Generation Sequence LIMS] - track and trace all GoNL samples and analysis (UMCG)
     23   * SequencingIntersection - Find shared variants among samples (UMCG)
     24 * '''Genotype analysis and imputation'''
     25   * [wiki:Imputations] - Work group main page
     26   * [wiki:PhenotypeAnalysis] - Work group main page
     27   * TrioAwarePhasingPipeline - phasing the individuals using trio information (EMC)
     28   * SnpAnnotationPipeline - annotating SNPs with known functional information (LUMC,UMCG)
     29   * ImputationPipeline - description of the imputation pipeline (VU,UMCG)
     30   * [http://www.bbmriwiki.nl/wiki/Impute2Pipeline Impute2Pipeline] - description of the Impute2 pipeline (UMCG)
     31   * AlleleCounting - count alleles accross a set of sample.vcf
     32 * '''Catalogue and search of biobanks'''
     33   * [http://www.phenoflow.org/wiki/BiobankCatalog Catalog of Dutch biobanks] - in collaboration with [https://wiki.nbic.nl/index.php/Biobanking NBIC biobanking task force]
     34   * [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]
     35 * '''Genomic biobank IT infrastructure'''
     36   * DataManagement - how we use MOLGENIS to track/trace data and tools (UMCG)
     37   * WorkflowTools - how to configure, manage and run pipelines (UMCG,AMC)
     38   * SequenceBIMS - to have report on samples, raw/intermediate/result data and processing pipelines run
     39   * GwasBIMS - to have report on samples, imputation runs and results
     40   * ApplyForDataTool - to provide researchers with a way to request access to BBMRI-NL data sets
     41   * BigStorage - how we store the NGS and GWAS data (UMCG,SARA,CIT)
     42   * BigCompute - how we will enable the pipelines on grids and clusters (UMCG,AMC,SARA,CIT)
    843
    944= Using this wiki =
     
    1752 * '''Browse source''' - All our scripts we can browsed under Browse Source
    1853 * '''Subversion''' - Programmers can commit their code using SVN at http://gbic.target.rug.nl/bbmri/svn
    19 
    2054= BBMRI projects are developed in collaboration with =
    2155