Exome Sequence from Ovarian cancer patient: Normal Blood: Sample 38fd7771-eaa7-4d4c-aea2-00fe7a_D1
Genomic DNA samples were used to prepare indexed libraries using the Nextera Rapid Capture Exome kit from Illumina. Library preparation was performed using a semi-automated 96-well plate method, with washing and clean-up/concentration steps performed on the Beckman Coulter Biomek NXP platform and with ZR-96 DNA Clean & Concentrator™-5 plates, respectively. Libraries were quantified using the Agilent 2100 Bioanalyzer. Pooled libraries were run on HiSeq4000 (2x150 paired end runs) to achieve a minimum of 150x on target coverage per each sample library. The raw Illumina sequence data were demultiplexed and converted to fastq files, adapter and low-quality sequences were trimmed. Paired-end WXS reads were aligned to the human reference genome (hg19) with BWA-mem (version 0.7.15-r1140). The bam files were further processed by adding read groups, marking duplicates, and re-ordering with Picard tools (version 2.9.0). Consequently, base quality score recalibration and INDEL realignment were performed using GATK modules IndelRealigner and BaseRecalibrator. The resulting bams were uploaded to short read archive.
NCI-phs000892
267_DN
alignment_software
BWA mem version 0.7.8-r744-dirty