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Background: Exome sequencing is a prospective method to discover genetic variations such as copy number variation (CNV), and therefore association studies could be carried out to explore the correlation with complex disease phenotypes.Compared with the whole genome sequencing that needs huge budget to achieve high sequencing coverage, the exome sequencing can meet the coverage requirement with limited portion of budget.Since the exons locate separately on the genome, and have distinct size, the analyzing tools that designed to whole genome sequencing cannot be employed to exome sequencing directly.It is of great importance to develop exome sequencing targeted methods.