Article
Effective filtering strategies to improve data quality from population-based whole exome sequencing studies.
BMC bioinformatics - 2 May 2014
Carson Andrew R, Smith Erin N, Matsui Hiroko, Brækkan Sigrid K, Jepsen Kristen, Hansen John-Bjarne, Frazer Kelly A
Abstract excerpt
BACKGROUND: Genotypes generated in next generation sequencing studies contain errors which can significantly impact the power to detect signals in common and rare variant association tests. These genotyping errors are not explicitly filtered by the standard GATK Variant Quality Score Recalibration (VQSR) tool and thus remain a source of errors in whole exome sequencing (WES) projects that follow GATK's...
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