ArticleGenomics, proteomics & bioinformatics2022
inGAP-family: Accurate Detection of Meiotic Recombination Loci and Causal Mutations by Filtering Out Artificial Variants due to Genome Complexities.
Article in Genomics, proteomics & bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- The deSUMOylase SPF2 and the cohesin regulators SGO2 and CTF18 suppress crossovers near centromeres.Nature plants · 2026Article
- Polymorphism can extensively reshape the genome-wide crossover landscape in Arabidopsis thaliana.Nature communications · 2026Article
- The regulatory mechanisms controlling meiotic cross-over patterning in plants.Biochemical Society transactions · 2025Review
- Maximizing meiotic crossover rates reveals the map of Crossover Potential.Nature communications · 2025Article
- MutLγ enforces meiotic crossovers in Arabidopsis thaliana.Nucleic acids research · 2025Article
- Enhanced recombination empowers the detection and mapping of Quantitative Trait Loci.Communications biology · 2024Article
- A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range.Nature genetics · 2024Article
- Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis.Genome biology · 2024Article
- SCEP1 and SCEP2 are two new components of the synaptonemal complex central element.Nature plants · 2023Article
- Article
- HEIP1 is required for efficient meiotic crossover implementation and is conserved from plants to humans.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- The nearly complete assembly of the Cercis chinensis genome and Fabaceae phylogenomic studies provide insights into new gene evolution.Plant communications · 2023Article
- High-frequency synthetic apomixis in hybrid rice.Nature communications · 2022Article
- Joint control of meiotic crossover patterning by the synaptonemal complex and HEI10 dosage.Nature communications · 2022Article
- The megabase-scale crossover landscape is largely independent of sequence divergence.Nature communications · 2022Article
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5 authors.
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Abstract
Accurately identifying DNA polymorphisms can bridge the gap between phenotypes and genotypes and is essential for molecular marker assisted genetic studies. Genome complexities, including large-scale structural variations, bring great challenges to bioinformatic analysis for obtaining high-confidence genomic variants, as sequence differences between non-allelic loci of two or more genomes can be misinterpreted as polymorphisms. It is important to correctly filter out artificial variants to avoid false genotyping or estimation of allele frequencies. Here, we present an efficient and effective framework, inGAP-family, to discover, filter, and visualize DNA polymorphisms and structural variants (SVs) from alignment of short reads. Applying this method to polymorphism detection on real datasets shows that elimination of artificial variants greatly facilitates the precise identification of meiotic recombination points as well as causal mutations in mutant genomes or quantitative trait loci. In addition, inGAP-family provides a user-friendly graphical interface for detecting polymorphisms and SVs, further evaluating predicted variants and identifying mutations related to genotypes. It is accessible at https://sourceforge.net/projects/ingap-family/.
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