ArticleBioMed research international2015
A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference.
Article in BioMed research international, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
- A universal indel filtering workflow for both long-read and short-read NGS data.BMC research notes · 2026Article
- Genomic insights into the population history of fat-tailed sheep and identification of two mutations that contribute to fat tail adipogenesis.Journal of advanced research · 2026Article
- Molecular Identification and RNA-Based Management of Fungal Plant Pathogens: From PCR to CRISPR/Cas9.International journal of molecular sciences · 2026Review
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows.Viruses · 2024Article
- A comparative investigation of single nucleotide variant calling for a personal non-Caucasian sequencing sample.Genes & genomics · 2023Article
- Evaluating the performance of low-frequency variant calling tools for the detection of variants from short-read deep sequencing data.Scientific reports · 2023Article
- Genetic testing in monogenic early-onset atrial fibrillation.European journal of human genetics : EJHG · 2023Article
- Evaluation of variant calling algorithms for wastewater-based epidemiology using mixed populations of SARS-CoV-2 variants in synthetic and wastewater samples.Microbial genomics · 2023Article
- Evaluation of an optimized germline exomes pipeline using BWA-MEM2 and Dragen-GATK tools.PloS one · 2023Article
- Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment.Scientific reports · 2022Article
- Evaluating the accuracy of variant calling methods using the frequency of parent-offspring genotype mismatch.Molecular ecology resources · 2022Article
- Accuracy benchmark of the GeneMind GenoLab M sequencing platform for WGS and WES analysis.BMC genomics · 2022Article
- The evaluation of Bcftools mpileup and GATK HaplotypeCaller for variant calling in non-human species.Scientific reports · 2022Article
- Establishment of reference standards for multifaceted mosaic variant analysis.Scientific data · 2022Article
- An evaluation of pipelines for DNA variant detection can guide a reanalysis protocol to increase the diagnostic ratio of genetic diseases.NPJ genomic medicine · 2022Article
- A rapid turnaround gene panel for severe autoinflammation: Genetic results within 48 hours.Frontiers in immunology · 2022Article
- A whole genome sequencing approach to anterior cruciate ligament rupture-a twin study in two unrelated families.PloS one · 2022Article
- Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels.BMC bioinformatics · 2021Article
- Review
5 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput sequencing, especially of exomes, is a popular diagnostic tool, but it is difficult to determine which tools are the best at analyzing this data. In this study, we use the NIST Genome in a Bottle results as a novel resource for validation of our exome analysis pipeline. We use six different aligners and five different variant callers to determine which pipeline, of the 30 total, performs the best on a human exome that was used to help generate the list of variants detected by the Genome in a Bottle Consortium. Of these 30 pipelines, we found that Novoalign in conjunction with GATK UnifiedGenotyper exhibited the highest sensitivity while maintaining a low number of false positives for SNVs. However, it is apparent that indels are still difficult for any pipeline to handle with none of the tools achieving an average sensitivity higher than 33% or a Positive Predictive Value (PPV) higher than 53%. Lastly, as expected, it was found that aligners can play as vital a role in variant detection as variant callers themselves.
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