= '''Overview BGI datasets''' =

TODO: More info on statistic and how to access the dataset will be added here.
BGI will shared with us: SNP calling results (VCF), SOAP format for indels.

|| '''Batch''' || '''Samples''' || '''Lanes''' || '''Size''' || '''Groningen storage''' || '''Grid storage (VO)''' || '''Storage additional sites''' || '''Analysis site''' || '''Status''' ||
|| 1st batch aka Pilot phase || 60 || 183 || || yes || yes (vlemed) || || UMGC, AMC (for comparison) || aligned, in progress ||
|| 2st batch || 90 || 295 || || yes || yes (vlemed) || || AMC || in progress ||
|| 3rd batch || 222 || 683 || 10TB || yes || no || || UMGC || in progress ||
|| 4th batch || 235 || 630 || 10TB || yes || yes (bbmri.nl) || Hubrecht, EMC || LUMC/TUdelft, UMGC, Hubrecht, EMC || in progress ||
|| 5th batch || 153 || || || no || no || || || not on storage yet ||
|| 6th batch || 10 || || || no || || || || not arrived yet ||

== '''Directories''' ==

'''1st batch'''
* Groningen
   * Raw data (fastq)
   * Results
* Grid (vlemed)
   * Raw data SRM (fastq) srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/vlemed/gvnl/data (access to members of vlemed/gvnl VO)
   * Raw data LFC (fastq) lfn://lfc.grid.sara.nl:5010/grid/vlemed/gvnl/data (access closed)
   * Results LFC lfn://lfc.grid.sara.nl:5010/grid/vlemed/gvnl/data/bam/markduplicates/realignment/fixmates/recalibrate/sorted (access closed)
   * Note: results will be copied to bbmri.nl VO when analysis is done

'''2nd batch'''
* Groningen
   * Raw data (fastq)
   * Results (bam)
* Grid (vlemed)
   * Raw data SRM (fastq) srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/vlemed/gvnl/data (access to members of vlemed/gvnl VO)
   * Raw data LFC (fastq) lfn://lfc.grid.sara.nl:5010/grid/vlemed/gvnl/data (access closed)
   * Results LFC lfn://lfc.grid.sara.nl:5010/grid/vlemed/gvnl/data/bam/markduplicates/realignment/fixmates/recalibrate/sorted (access closed)
   * Note: results will be copied to bbmri.nl VO when analysis is done

'''3rd batch'''
* Groningen
   * Raw data (fastq)
   * Results


'''4th batch'''
* Groningen
   * Raw data (fastq)
   * Results
* Grid (bbmri.nl)
   * Raw data SRM (fastq) srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/bbmri.nl/fourth_batch (access to members of bbmri.nl VO)
   * Raw data LFC (fastq) lfn://lfc.grid.sara.nl:5010/grid/bbmri.nl/gonl/data/input (access to members of bbmri.nl VO)
   * Results LFC lfn://lfc.grid.sara.nl:5010/grid/bbmri.nl/gonl/data/output (access to members of bbmri.nl VO)