{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,6]],"date-time":"2025-08-06T12:33:35Z","timestamp":1754483615278},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: A review of the available single nucleotide polymorphism (SNP) calling procedures for Illumina high-throughput sequencing (HTS) platform data reveals that most rely mainly on base-calling and mapping qualities as sources of error when calling SNPs. Thus, errors not involved in base-calling or alignment, such as those in genomic sample preparation, are not accounted for.<\/jats:p>\n               <jats:p>Results: A novel method of consensus and SNP calling, Genotype Model Selection (GeMS), is given which accounts for the errors that occur during the preparation of the genomic sample. Simulations and real data analyses indicate that GeMS has the best performance balance of sensitivity and positive predictive value among the tested SNP callers.<\/jats:p>\n               <jats:p>Availability: The GeMS package can be downloaded from https:\/\/sites.google.com\/a\/bioinformatics.ucr.edu\/xinping-cui\/home\/software or http:\/\/computationalbioenergy.org\/software.html<\/jats:p>\n               <jats:p>Contact: \u00a0xinping.cui@ucr.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts001","type":"journal-article","created":{"date-parts":[[2012,1,18]],"date-time":"2012-01-18T02:33:15Z","timestamp":1326853995000},"page":"643-650","source":"Crossref","is-referenced-by-count":20,"title":["SNP calling using genotype model selection on high-throughput sequencing data"],"prefix":"10.1093","volume":"28","author":[{"given":"Na","family":"You","sequence":"first","affiliation":[{"name":"1 Department of Statistical Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275, China, 2Department of Statistics, University of California, Riverside, CA 92521, USA, 3Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China, 4Plant Stress Genomic and Technology Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia, 5Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907,USA and 6Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA"}]},{"given":"Gabriel","family":"Murillo","sequence":"additional","affiliation":[{"name":"1 Department of Statistical Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275, China, 2Department of Statistics, University of California, Riverside, CA 92521, USA, 3Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China, 4Plant Stress Genomic and Technology Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia, 5Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907,USA and 6Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA"}]},{"given":"Xiaoquan","family":"Su","sequence":"additional","affiliation":[{"name":"1 Department of Statistical Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275, China, 2Department of Statistics, University of California, Riverside, CA 92521, USA, 3Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China, 4Plant Stress Genomic and Technology Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia, 5Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907,USA and 6Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA"}]},{"given":"Xiaowei","family":"Zeng","sequence":"additional","affiliation":[{"name":"1 Department of Statistical Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275, China, 2Department of Statistics, University of California, Riverside, CA 92521, USA, 3Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China, 4Plant Stress Genomic and Technology Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia, 5Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907,USA and 6Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA"}]},{"given":"Jian","family":"Xu","sequence":"additional","affiliation":[{"name":"1 Department of Statistical Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275, China, 2Department of Statistics, University of California, Riverside, CA 92521, USA, 3Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China, 4Plant Stress Genomic and Technology Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia, 5Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907,USA and 6Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA"}]},{"given":"Kang","family":"Ning","sequence":"additional","affiliation":[{"name":"1 Department of Statistical Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275, China, 2Department of Statistics, University of California, Riverside, CA 92521, USA, 3Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China, 4Plant Stress Genomic and Technology Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia, 5Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907,USA and 6Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA"}]},{"given":"Shoudong","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Department of Statistical Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275, China, 2Department of Statistics, University of California, Riverside, CA 92521, USA, 3Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China, 4Plant Stress Genomic and Technology Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia, 5Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907,USA and 6Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA"}]},{"given":"Jiankang","family":"Zhu","sequence":"additional","affiliation":[{"name":"1 Department of Statistical Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275, China, 2Department of Statistics, University of California, Riverside, CA 92521, USA, 3Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China, 4Plant Stress Genomic and Technology Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia, 5Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907,USA and 6Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA"},{"name":"1 Department of Statistical Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275, China, 2Department of Statistics, University of California, Riverside, CA 92521, USA, 3Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China, 4Plant Stress Genomic and Technology Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia, 5Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907,USA and 6Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA"}]},{"given":"Xinping","family":"Cui","sequence":"additional","affiliation":[{"name":"1 Department of Statistical Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275, China, 2Department of Statistics, University of California, Riverside, CA 92521, USA, 3Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China, 4Plant Stress Genomic and Technology Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia, 5Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907,USA and 6Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA"},{"name":"1 Department of Statistical Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275, China, 2Department of Statistics, University of California, Riverside, CA 92521, USA, 3Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China, 4Plant Stress Genomic and Technology Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia, 5Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907,USA and 6Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA"}]}],"member":"286","published-online":{"date-parts":[[2012,1,16]]},"reference":[{"key":"2023012512192588400_B1","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1101\/gr.112326.110","article-title":"Dindel: accurate indel calls from short-read data","volume":"21","author":"Albers","year":"2011","journal-title":"Genome 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