Article
Empirical design of a variant quality control pipeline for whole genome sequencing data using replicate discordance.
Scientific reports - 6 Nov 2019
Adelson Robert P, Renton Alan E, Li Wentian, Barzilai Nir, Atzmon Gil, Goate Alison M, Davies Peter, Freudenberg-Hua Yun
Abstract excerpt
The success of next-generation sequencing depends on the accuracy of variant calls. Few objective protocols exist for QC following variant calling from whole genome sequencing (WGS) data. After applying QC filtering based on Genome Analysis Tool Kit (GATK) best practices, we used genotype discordance of eight samples that were sequenced twice each to evaluate the proportion of potentially inaccurate variant...
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