ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2017
Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Bioinformatics in crop research: using genomic data for crop improvement.Frontiers in plant science · 2026Review
- The Eastern Fox Squirrel (Journal of mammalogy · 2025Article
- Characterization of quantitative trait loci from DJ123 (Molecular breeding : new strategies in plant improvement · 2024Article
- Novel QTL for Lateral Root Density and Length Improve Phosphorus Uptake in Rice (Oryza sativa L.).Rice (New York, N.Y.) · 2023Article
- Multispectral Phenotyping and Genetic Analyses of Spring Appearance in Greening Plant,Plant phenomics (Washington, D.C.) · 2023Article
- QTL mapping for early root and shoot vigor of upland rice (Frontiers in plant science · 2022Article
- Genomic signatures of natural selection at phenology-related genes in a widely distributed tree species Fagus sylvatica L.BMC genomics · 2021Article
- Genetic dissection of QTLs associated with spikelet-related traits and grain size in sorghum.Scientific reports · 2021Article
- Dissecting the Genetic Architecture of Biofuel-Related Traits in a Sorghum Breeding Population.G3 (Bethesda, Md.) · 2020Article
- Impacts of dominance effects on genomic prediction of sorghum hybrid performance.Breeding science · 2020Article
- A Fast and Scalable Workflow for SNPs Detection in Genome Sequences Using Hadoop Map-Reduce.Genes · 2020Article
- Comparison of shape quantification methods for genomic prediction, and genome-wide association study of sorghum seed morphology.PloS one · 2019Article
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent availability of large-scale genomic resources enables us to conduct so called genome-wide association studies (GWAS) and genomic prediction (GP) studies, particularly with next-generation sequencing (NGS) data. The effectiveness of GWAS and GP depends on not only their mathematical models, but the quality and quantity of variants employed in the analysis. In NGS single nucleotide polymorphism (SNP) calling, conventional tools ideally require more reads for higher SNP sensitivity and accuracy. In this study, we aimed to develop a tool, Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both ends of reads or containing a minor allele supported by only one read. Performance comparison with existing tools showed that Heap achieved the highest F-scores with low coverage (7X) restriction-site associated DNA sequencing reads of sorghum and rice individuals. This will facilitate cost-effective GWAS and GP studies in this NGS era. Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap (29 March 2017, date last accessed) and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html (29 March 2017, date last accessed)).
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