Empirical design of a variant quality control pipeline for whole genome sequencing data using replicate discordance

Robert P. Adelson, Alan E. Renton, Wentian Li, Nir Barzilai, Gil Atzmon, Alison M. Goate, Peter Davies, Yun Freudenberg-Hua

Research output: Contribution to journalArticlepeer-review


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 calls. We designed a QC pipeline involving hard filters to improve replicate genotype concordance, which indicates improved accuracy of genotype calls. Our pipeline analyzes the efficacy of each filtering step. We initially applied this strategy to well-characterized variants from the ClinVar database, and subsequently to the full WGS dataset. The genome-wide biallelic pipeline removed 82.11% of discordant and 14.89% of concordant genotypes, and improved the concordance rate from 98.53% to 99.69%. The variant-level read depth filter most improved the genome-wide biallelic concordance rate. We also adapted this pipeline for triallelic sites, given the increasing proportion of multiallelic sites as sample sizes increase. For triallelic sites containing only SNVs, the concordance rate improved from 97.68% to 99.80%. Our QC pipeline removes many potentially false positive calls that pass in GATK, and may inform future WGS studies prior to variant effect analysis.

Original languageEnglish
Article number16156
JournalScientific Reports
Issue number1
StatePublished - 1 Dec 2019

Bibliographical note

Funding Information:
We thank the study participants and the staff members at the Albert Einstein College of Medicine, the Feinstein Institute for Medical Research, and the National Institute on Aging Genetics Initiative for Late-Onset Alzheimer Disease/National Cell Repository for Alzheimer Disease (NIA-LOAD/NCRAD) for their contributions to this study. We also thank Erica Christen, Manav Kapoor, Edoardo Marcora, Brian Fulton-Howard, Ronak H. Shah, Avinash Abhyankar, and Jan Freudenberg for sequencing data processing, organization, and helpful discussions integral to this project. This project is supported by the Mildred and Frank Feinberg Family Foundation. Y.F.H. is supported by National Institutes of Health/National Institute on Aging grant K08AG054727. N.B. and G.A. are supported by National Institutes of Health/National Institute on Aging grants R01 AG 618381, R01 AG 042188, R01 AG 046949, and P01 AG 021654, the Einstein Nathan Shock Center grant P30AG038072, and the Glenn Center for the Biology of Human Aging.

Publisher Copyright:
© 2019, The Author(s).

ASJC Scopus subject areas

  • General


Dive into the research topics of 'Empirical design of a variant quality control pipeline for whole genome sequencing data using replicate discordance'. Together they form a unique fingerprint.

Cite this