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e-BioGrid project for biobanking started
We have proudly joined the e-BioGrid project on a mission to bring nation-wide IT infrastructure for large scale biobanking. First goal is building a model infrastructure for the Dutch Biobank community, BBMRI-NL, that manage ...
Proposed Quality Control.
Pre-alignment:
- Duplicate input checking.
- Quality scores histogram from the BGI.
- Maybe other graphs/data provided by the BGI.
- Quality scores with the FastqC toolkit.
- GC content.
- Quality scores per base.
- Quality scores per ...
Hackathon on pipelines, grid and QC
Yesterday we had a succesfull joint hackathon in Haren accross BBMRI-NL bioinformatics and NBIC biobank and next generation sequencing task forces. Representatives were there from UMCG, AMC, LUMC and NBIC as well as guests of the local genomics coord ...
First raw reads in; Freerk and Morris go to Boston to get GATK running
The first two trio data has been downloaded from BGI. Meanwhile BGI is running the basic analysis, i.e., variant calling on the whole batch. Freerk and Morris went to Boston to learn how to do the same procedure but then using GATK. Hopefully by end ...
BBMRI-NL Rainbow projects:
- RP3 - The BIOS Consortium (Biobank-based Integrative Omics Studies) (private)
- The BIOS Consortium (Biobank-based Integrative Omics Studies)
To gain access to restricted areas (RP3) please fill in a code of conduct (please contact Bas Heijmans for this CoC, b.t.heijmans AT lumc.nl) Send after approval an email to the GCC helpdesk to get an account (helpdesk.gcc.groningen AT gmail.com) For RP2 please contact: m.a.swertz AT rug.nl or pieter.neerincx AT gmail.com (for RP2)
SOPs and Pipelines:
- Sequence analysis
- 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
- 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
- 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
- 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)
Using this wiki
As all Wiki pages, this page is editable, this means that you can modify the contents of this page simply by using your web-browser. Simply click on the "Edit this page" link at the bottom of the page. WikiFormatting will give you a detailed description of available Wiki formatting commands.
On top there is menu with additional features
- Blog - Meetings, events etc can be blogged
- Roadmap - Overview of the main objectives
- Tickets - All our TODO's (per roadmap) we can collect under Tickets
- Browse source - All our scripts we can browsed under Browse Source
- Subversion - Programmers can commit their code using SVN at http://gbic.target.rug.nl/bbmri/svn
BBMRI projects are developed in collaboration with
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