{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:59Z","timestamp":1772138039171,"version":"3.50.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2020,5,29]],"date-time":"2020-05-29T00:00:00Z","timestamp":1590710400000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Biotechnology and Biological Sciences Research Council ISPG to the Roslin Institute","award":["BB\/J004235\/1"],"award-info":[{"award-number":["BB\/J004235\/1"]}]},{"name":"Biotechnology and Biological Sciences Research Council ISPG to the Roslin Institute","award":["BB\/M009254\/1"],"award-info":[{"award-number":["BB\/M009254\/1"]}]},{"name":"Biotechnology and Biological Sciences Research Council ISPG to the Roslin Institute","award":["BB\/L020726\/1"],"award-info":[{"award-number":["BB\/L020726\/1"]}]},{"name":"Biotechnology and Biological Sciences Research Council ISPG to the Roslin Institute","award":["BB\/N004736\/1"],"award-info":[{"award-number":["BB\/N004736\/1"]}]},{"name":"Biotechnology and Biological Sciences Research Council ISPG to the Roslin Institute","award":["BB\/N004728\/1"],"award-info":[{"award-number":["BB\/N004728\/1"]}]},{"name":"Biotechnology and Biological Sciences Research Council ISPG to the Roslin Institute","award":["BB\/L020467\/1"],"award-info":[{"award-number":["BB\/L020467\/1"]}]},{"name":"Biotechnology and Biological Sciences Research Council ISPG to the Roslin Institute","award":["BB\/N006178\/1"],"award-info":[{"award-number":["BB\/N006178\/1"]}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"MRC","doi-asserted-by":"publisher","award":["MR\/M000370\/1"],"award-info":[{"award-number":["MR\/M000370\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>AlphaFamImpute 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 na\u00efve 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 &amp;lt;1x coverage.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>AlphaFamImpute is available as a Python package from the AlphaGenes website http:\/\/www.AlphaGenes.roslin.ed.ac.uk\/AlphaFamImpute.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa499","type":"journal-article","created":{"date-parts":[[2020,5,25]],"date-time":"2020-05-25T07:08:09Z","timestamp":1590390489000},"page":"4369-4371","source":"Crossref","is-referenced-by-count":17,"title":["AlphaFamImpute: high-accuracy imputation in full-sib families from genotype-by-sequencing data"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6922-0947","authenticated-orcid":false,"given":"Andrew","family":"Whalen","sequence":"first","affiliation":[{"name":"The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh , Midlothian EH25 9RG, UK"}]},{"given":"Gregor","family":"Gorjanc","sequence":"additional","affiliation":[{"name":"The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh , Midlothian EH25 9RG, UK"}]},{"given":"John M","family":"Hickey","sequence":"additional","affiliation":[{"name":"The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh , Midlothian EH25 9RG, UK"}]}],"member":"286","published-online":{"date-parts":[[2020,5,28]]},"reference":[{"key":"2023062312042226600_btaa499-B1","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/s12711-017-0300-y","article-title":"A hybrid method for the imputation of genomic data in livestock populations","volume":"49","author":"Antol\u00edn","year":"2017","journal-title":"Genet. Sel. Evol"},{"key":"2023062312042226600_btaa499-B2","doi-asserted-by":"crossref","first-page":"e3376","DOI":"10.1371\/journal.pone.0003376","article-title":"Rapid SNP discovery and genetic mapping using sequenced RAD markers","volume":"3","author":"Baird","year":"2008","journal-title":"PLoS One"},{"key":"2023062312042226600_btaa499-B3","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1016\/j.ajhg.2009.01.005","article-title":"A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals","volume":"84","author":"Browning","year":"2009","journal-title":"Am. J. Hum. Genet"},{"key":"2023062312042226600_btaa499-B4","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1101\/gr.083634.108","article-title":"Fast and flexible simulation of DNA sequence data","volume":"19","author":"Chen","year":"2009","journal-title":"Genome Research"},{"key":"2023062312042226600_btaa499-B5","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/nrg3012","article-title":"Genome-wide genetic marker discovery and genotyping using next-generation sequencing","volume":"12","author":"Davey","year":"2011","journal-title":"Nat. Rev. Genet"},{"key":"2023062312042226600_btaa499-B6","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1038\/ng.3594","article-title":"Rapid genotype imputation from sequence without reference panels","volume":"48","author":"Davies","year":"2016","journal-title":"Nat. Genet"},{"key":"2023062312042226600_btaa499-B7","doi-asserted-by":"crossref","first-page":"e19379","DOI":"10.1371\/journal.pone.0019379","article-title":"A robust, simple genotyping-by-sequencing (GBS) approach\u00a0for high diversity species","volume":"6","author":"Elshire","year":"2011","journal-title":"PLoS One"},{"key":"2023062312042226600_btaa499-B8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1297-9686-46-11","article-title":"Detection of recombination events, haplotype reconstruction\u00a0and imputation of sires using half-sib SNP genotypes","volume":"46","author":"Ferdosi","year":"2014","journal-title":"Genet. Sel. 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