ArticleNucleic acids research2014
Performance comparison of SNP detection tools with illumina exome sequencing data--an assessment using both family pedigree information and sample-matched SNP array data.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- A comprehensive catalog of single nucleotide polymorphisms (SNPs) from the black pepper (Piper nigrum L.) genome.BMC genomics · 2025Article
- Limitations in next-generation sequencing-based genotyping of breast cancer polygenic risk score loci.European journal of human genetics : EJHG · 2024Article
- Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank.Nature genetics · 2023Article
- The evaluation of Bcftools mpileup and GATK HaplotypeCaller for variant calling in non-human species.Scientific reports · 2022Article
- Simulation of African and non-African low and high coverage whole genome sequence data to assess variant calling approaches.Briefings in bioinformatics · 2021Article
- Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels.BMC bioinformatics · 2021Article
- AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data.Nature communications · 2021Article
- Set-theory based benchmarking of three different variant callers for targeted sequencing.BMC bioinformatics · 2021Article
- DeepVariant-on-Spark: Small-Scale Genome Analysis Using a Cloud-Based Computing Framework.Computational and mathematical methods in medicine · 2020Article
- Performance assessment of variant calling pipelines using human whole exome sequencing and simulated data.BMC bioinformatics · 2019Article
- Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitative Trait Loci Detection.The plant genome · 2019Article
- Genotyping of Multiple Clinical Samples with a Combined Direct PCR and Magnetic Lateral Flow Assay.iScience · 2018Article
- Optimized Method of Extracting Rice Chloroplast DNA for High-Quality Plastome Resequencing andFrontiers in plant science · 2018Article
- A framework for the estimation of the proportion of true discoveries in single nucleotide variant detection studies for human data.PloS one · 2018Article
- SeqVItA: Sequence Variant Identification and Annotation Platform for Next Generation Sequencing Data.Frontiers in genetics · 2018Article
- Lightning-fast genome variant detection with GROM.GigaScience · 2017Article
- Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide: evidence for altered glial, endothelial and ATPase activity.Molecular psychiatry · 2017Article
- PEMapper and PECaller provide a simplified approach to whole-genome sequencing.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- An analytical workflow for accurate variant discovery in highly divergent regions.BMC genomics · 2016Article
- Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success.BMC research notes · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
To apply exome-seq-derived variants in the clinical setting, there is an urgent need to identify the best variant caller(s) from a large collection of available options. We have used an Illumina exome-seq dataset as a benchmark, with two validation scenarios--family pedigree information and SNP array data for the same samples, permitting global high-throughput cross-validation, to evaluate the quality of SNP calls derived from several popular variant discovery tools from both the open-source and commercial communities using a set of designated quality metrics. To the best of our knowledge, this is the first large-scale performance comparison of exome-seq variant discovery tools using high-throughput validation with both Mendelian inheritance checking and SNP array data, which allows us to gain insights into the accuracy of SNP calling through such high-throughput validation in an unprecedented way, whereas the previously reported comparison studies have only assessed concordance of these tools without directly assessing the quality of the derived SNPs. More importantly, the main purpose of our study was to establish a reusable procedure that applies high-throughput validation to compare the quality of SNP discovery tools with a focus on exome-seq, which can be used to compare any forthcoming tool(s) of interest.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.