Empirical design of a variant quality control pipeline for whole genome sequencing data using replicate discordance
Autor: | Nir Barzilai, Peter Davies, Robert P. Adelson, Alan E. Renton, Alison Goate, Yun Freudenberg-Hua, Gil Atzmon, Wentian Li |
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Jazyk: | angličtina |
Rok vydání: | 2019 |
Předmět: |
Quality Control
Genotype Genotyping Techniques Pipeline (computing) Concordance lcsh:Medicine Datasets as Topic Computational biology Biology Genome Polymorphism Single Nucleotide Article 03 medical and health sciences 0302 clinical medicine Databases Genetic Humans Genetic variation lcsh:Science Alleles 030304 developmental biology Whole genome sequencing 0303 health sciences Multidisciplinary Whole Genome Sequencing lcsh:R High-Throughput Nucleotide Sequencing Reproducibility of Results Replicate Empirical design Sample size determination Next-generation sequencing lcsh:Q 030217 neurology & neurosurgery |
Zdroj: | Scientific Reports Scientific Reports, Vol 9, Iss 1, Pp 1-12 (2019) |
ISSN: | 2045-2322 |
Popis: | 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. |
Databáze: | OpenAIRE |
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