ArticleGenome research2013
An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
57 citing papers in PubMed.
- Article
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- Dissecting biological heterogeneity in major depressive disorder based on neuroimaging subtypes with multi-omics data.Translational psychiatry · 2025Article
- Bridging animal models and humans: neuroimaging as intermediate phenotypes linking genetic or stress factors to anhedonia.BMC medicine · 2025Article
- Linked Selection and Gene Density Shape Genome-Wide Patterns of Diversification in Peatmosses.Evolutionary applications · 2024Article
- Genetic association analysis of human median voice pitch identifies a common locus for tonal and non-tonal languages.Communications biology · 2024Article
- Associations between polygenic risk scores and accelerated brain ageing in smokers.Psychological medicine · 2023Article
- Article
- How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a microendemic Malagasy tree.Molecular ecology · 2023Article
- Genotype calling and haplotype inference from low coverage sequence data in heterozygous plant genome using HetMap.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Article
- Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep.Communications biology · 2021Article
- A consensus and saturated genetic map provides insight into genome anchoring, synteny of Solanaceae and leaf- and fruit-related QTLs in wolfberry (Lycium Linn.).BMC plant biology · 2021Article
- Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus.Molecular biology and evolution · 2021Article
- Ancient mitochondrial genomes from Chinese cave hyenas provide insights into the evolutionary history of the genusProceedings. Biological sciences · 2021Article
- Identification of Novel Single-Nucleotide Variants With Potential of Mediating Malfunction of MicroRNA in Congenital Heart Disease.Frontiers in cardiovascular medicine · 2021Article
- Polygenic risk for autism spectrum disorder affects left amygdala activity and negative emotion in schizophrenia.Translational psychiatry · 2020Article
- Heavy reliance on plants for Romanian cave bears evidenced by amino acid nitrogen isotope analysis.Scientific reports · 2020Article
- Pathway-based polygene risk for severe depression implicates drug metabolism in CONVERGE.Psychological medicine · 2020Article
- Reduced meiotic recombination in rhesus macaques and the origin of the human recombination landscape.PloS one · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Next-generation sequencing is a powerful approach for discovering genetic variation. Sensitive variant calling and haplotype inference from population sequencing data remain challenging. We describe methods for high-quality discovery, genotyping, and phasing of SNPs for low-coverage (approximately 5×) sequencing of populations, implemented in a pipeline called SNPTools. Our pipeline contains several innovations that specifically address challenges caused by low-coverage population sequencing: (1) effective base depth (EBD), a nonparametric statistic that enables more accurate statistical modeling of sequencing data; (2) variance ratio scoring, a variance-based statistic that discovers polymorphic loci with high sensitivity and specificity; and (3) BAM-specific binomial mixture modeling (BBMM), a clustering algorithm that generates robust genotype likelihoods from heterogeneous sequencing data. Last, we develop an imputation engine that refines raw genotype likelihoods to produce high-quality phased genotypes/haplotypes. Designed for large population studies, SNPTools' input/output (I/O) and storage aware design leads to improved computing performance on large sequencing data sets. We apply SNPTools to the International 1000 Genomes Project (1000G) Phase 1 low-coverage data set and obtain genotyping accuracy comparable to that of SNP microarray.
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Registered trials
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.