Identification of missing variants by combining multiple analytic pipelines.

ABSTRACT: BACKGROUND:After decades of identifying risk factors using array-based genome-wide association studies (GWAS), genetic research of complex diseases has shifted to sequencing-based rare variants discovery. This requires large sample sizes for statistical power and has brought up questions about whether the current variant calling practices are adequate for large cohorts. It is well-known that there are discrepancies between variants called by different pipelines, and that using a single pipeline always misses true variants exclusively identifiable by other pipelines. Nonetheless, it is common practice today to call variants by one pipeline due to computational cost and assume that false negative calls are a small percent of total. RESULTS:We analyzed 10,000 exomes from the Alzheimer's Disea

SUBMITTER: Ren Y 

PROVIDER: S-EPMC5902939 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature