Hiseq control software real time analysis

Genomic DNA was extracted by standard procedures from peripheral blood or Epstein–Barr virus immortalised lymphocytes. Concentration of DNAs for whole exome sequencing was measured using a Qubit V.2.0 Fluorometer (Life Technologies, Carlsbad, California, USA). Whole exome sequencing was performed as previously described.^{6 (link)7 (link)} Briefly, DNA (3 μg) was sheared by Covaris S2 system (Covaris, Wobum, Massachusetts, USA) and processed by SureSelectXT Human All Exon V5 (Agilent Technologies, Santa Clara, California, USA). Captured DNA was sequenced using HiSeq 2000 (Illumina, San Diego, California, USA) with 101 bp pair-end reads with seven indices. Image analysis and base calling were performed using HiSeq Control Software/Real-time analysis and CASAVA 1.8.2 (Illumina). Reads were mapped to the reference human genome (hg19) by Novoalign-3.02.04. Aligned reads were processed by Picard to remove PCR duplicates. Variants were called by Genome Analysis Toolkit (GATK) v2.7-4 based on GATK Best Practice Workflow v3 and annotated by ANNOVAR (downloaded at 2013 June).