= 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 = 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