ArticleScientific reports2019
Empirical design of a variant quality control pipeline for whole genome sequencing data using replicate discordance.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Population-scale cross-disorder atlas of the human prefrontal cortex at single-cell resolution.Scientific data · 2025Article
- A sequence context-based approach for classifying tumor structural variants without paired normal samples.Cell reports methods · 2025Article
- A multi-region single nucleus transcriptomic atlas of Parkinson's disease.Scientific data · 2024Article
- Semi-supervised machine learning method for predicting homogeneous ancestry groups to assess Hardy-Weinberg equilibrium in diverse whole-genome sequencing studies.American journal of human genetics · 2024Article
- Biostatistical Aspects of Whole Genome Sequencing Studies: Preprocessing and Quality Control.Biometrical journal. Biometrische Zeitschrift · 2024Article
- Comparison of germline and somatic structural variants in cancers reveal systematic differences in variant generating and selection processes.bioRxiv : the preprint server for biology · 2024Article
- Discordant calls across genotype discovery approaches elucidate variants with systematic errors.Genome research · 2023Article
- The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication.G3 (Bethesda, Md.) · 2023Article
- FVC as an adaptive and accurate method for filtering variants from popular NGS analysis pipelines.Communications biology · 2022Article
- Challenges at the APOE locus: a robust quality control approach for accurate APOE genotyping.Alzheimer's research & therapy · 2022Article
- Nucleotide-based genetic networks: Methods and applications.Journal of biosciences · 2022Article
- Detecting Genetic Ancestry and Adaptation in the Taiwanese Han People.Molecular biology and evolution · 2021Article
- Greater effect of polygenic risk score for Alzheimer's disease among younger cases who are apolipoprotein E-ε4 carriers.Neurobiology of aging · 2021Article
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Authors and funding
8 authors.
Funding
Abstract
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.
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