Notes meeting 27-10-2010

Ideas

• 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

Questions

• 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

Grid

• Two options:
• Commandline
• Workflow