Novel metrics to measure coverage in whole exome sequencing datasets reveal local and global non-uniformity.

ABSTRACT: Whole Exome Sequencing (WES) is a powerful clinical diagnostic tool for discovering the genetic basis of many diseases. A major shortcoming of WES is uneven coverage of sequence reads over the exome targets contributing to many low coverage regions, which hinders accurate variant calling. In this study, we devised two novel metrics, Cohort Coverage Sparseness (CCS) and Unevenness (U_E) Scores for a detailed assessment of the distribution of coverage of sequence reads. Employing these metrics we revealed non-uniformity of coverage and low coverage regions in the WES data generated by three different platforms. This non-uniformity of coverage is both local (coverage of a given exon across different platforms) and global (coverage of all exons across the genome in the given platform

SUBMITTER: Wang Q 

PROVIDER: S-EPMC5429826 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature