ArticleBioinformatics (Oxford, England)2020
AlphaFamImpute: high-accuracy imputation in full-sib families from genotype-by-sequencing data.
Article in Bioinformatics (Oxford, England), 2020. 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, 43 citations in OpenAlex.
- Article
- Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR.The plant genome · 2024Article
- Reconstructing parent genomes using siblings and other relatives.bioRxiv : the preprint server for biology · 2024Article
- A cautionary tale of low-pass sequencing and imputation with respect to haplotype accuracy.Genetics, selection, evolution : GSE · 2024Article
- Article
- QTL mapping of almond kernel quality traits in the FFrontiers in plant science · 2024Article
- Genome-wide allele frequency studies in Pacific oyster families identify candidate genes for tolerance to ostreid herpesvirus 1 (OsHV-1).BMC genomics · 2023Article
- Imputation of low-density marker chip data in plant breeding: Evaluation of methods based on sugar beet.The plant genome · 2022Article
- Mendelian imputation of parental genotypes improves estimates of direct genetic effects.Nature genetics · 2022Article
- Chromosome evolution and the genetic basis of agronomically important traits in greater yam.Nature communications · 2022Article
- Effects of common full-sib families on accuracy of genomic prediction for tagging weight in striped catfishFrontiers in genetics · 2022Article
- Genotyping, the Usefulness of Imputation to Increase SNP Density, and Imputation Methods and Tools.Methods in molecular biology (Clifton, N.J.) · 2022Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
summaryAlphaFamImpute is an imputation package for calling, phasing and imputing genome-wide genotypes in outbred full-sib families from single nucleotide polymorphism (SNP) array and genotype-by-sequencing (GBS) data. GBS data are increasingly being used to genotype individuals, especially when SNP arrays do not exist for a population of interest. Low-coverage GBS produces data with a large number of missing or incorrect naïve genotype calls, which can be improved by identifying shared haplotype segments between full-sib individuals. Here, we present AlphaFamImpute, an algorithm specifically designed to exploit the genetic structure of full-sib families. It performs imputation using a two-step approach. In the first step, it phases and imputes parental genotypes based on the segregation states of their offspring (i.e. which pair of parental haplotypes the offspring inherited). In the second step, it phases and imputes the offspring genotypes by detecting which haplotype segments the offspring inherited from their parents. With a series of simulations, we find that AlphaFamImpute obtains high-accuracy genotypes, even when the parents are not genotyped and individuals are sequenced at <1x coverage. AVAILABILITY AND IMPLEMENTATION: AlphaFamImpute is available as a Python package from the AlphaGenes website http://www.AlphaGenes.roslin.ed.ac.uk/AlphaFamImpute. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.