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)
  • 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)

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)

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)