Version 5 (modified by freerkvandijk, 12 years ago) (diff)


Notes meeting 27-10-2010


  • Have a look at Lisa/Huygens? cluster/grid
  • LISA -> M. Kattenberg will have a look
  • Phillips cluster could be an option
  • Leiden has shark cluster, 108 cpu's
  • If all trios put together for SNP calling etc. have a look for repeated error patterns in Illumina machines
  • Have a look at indel positions after calling, is position correct?

Action points

  • Put BGI lab protocol on wiki, insertsizes etc
  • Do check for interference etc
  • Solve I/O issues by next week
  • Add Pindel to pipeline


  • Is QC recalibration also needed for other platforms?

Pipeline Utrecht

  • Raw data
  • Split by barcodes/samples
  • Chunking and coversion to fastq
  • Fastq sent to nodes
  • Nodes return sorted .BAMs and statistics
  • Main node merges all data from other nodes
  • Custom pileup script merges (Frans-Paul)
  • Annotation
  • Query ENSEMBL from cluster nodes
  • Main node merges all output, filter on region of interest, put result in database
  • SNP calling
  • GATK in progress
  • VarScan? (Lot of false positives, not good enough)
  • Ask Frans for info


  • Two options:
  • Commandline
  • Workflow