The test blood DNA sample was whole genome sequenced on 7 lanes of Illumina HiSeq 2000.
The whole genome library was handled exactly as the exome enrichment libraries were for sequencing on the HiSeq 2000 (see “Exome Sequencing by Illumina HiSeq 2000” section). The whole genome library was run on seven lanes of HiSeq (with lane 5 of reserved for PhiX control). This yielded more than one billion total raw reads. Reads were aligned with BWA using the -q 30 parameter and duplicates were removed with Picard.