{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T23:44:12Z","timestamp":1776210252761,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: zCall is a variant caller specifically designed for calling rare single-nucleotide polymorphisms from array-based technology. This caller is implemented as a post-processing step after a default calling algorithm has been applied. The algorithm uses the intensity profile of the common allele homozygote cluster to define the location of the other two genotype clusters. We demonstrate improved detection of rare alleles when applying zCall to samples that have both Illumina Infinium HumanExome BeadChip and exome sequencing data available.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/atguweb.mgh.harvard.edu\/apps\/zcall.<\/jats:p>\n               <jats:p>Contact: \u00a0bneale@broadinstitute.org<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts479","type":"journal-article","created":{"date-parts":[[2012,7,29]],"date-time":"2012-07-29T00:55:19Z","timestamp":1343523319000},"page":"2543-2545","source":"Crossref","is-referenced-by-count":189,"title":["zCall: a rare variant caller for array-based genotyping"],"prefix":"10.1093","volume":"28","author":[{"given":"Jacqueline I.","family":"Goldstein","sequence":"first","affiliation":[{"name":"1 Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, 2Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 3Genetic Analysis Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 4Division of Psychiatric Genomics, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY 10029, 5Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 6Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 7Department of Genetics, Harvard Medical School, Boston, MA 02115 and 8Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27514, USA"},{"name":"1 Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, 2Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 3Genetic Analysis Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 4Division of Psychiatric Genomics, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY 10029, 5Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 6Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 7Department of Genetics, Harvard Medical School, Boston, MA 02115 and 8Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27514, USA"}]},{"given":"Andrew","family":"Crenshaw","sequence":"additional","affiliation":[{"name":"1 Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, 2Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 3Genetic Analysis Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 4Division of Psychiatric Genomics, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY 10029, 5Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 6Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 7Department of Genetics, Harvard Medical School, Boston, MA 02115 and 8Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27514, USA"}]},{"given":"Jason","family":"Carey","sequence":"additional","affiliation":[{"name":"1 Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, 2Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 3Genetic Analysis Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 4Division of Psychiatric Genomics, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY 10029, 5Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 6Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 7Department of Genetics, Harvard Medical School, Boston, MA 02115 and 8Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27514, USA"}]},{"given":"George B.","family":"Grant","sequence":"additional","affiliation":[{"name":"1 Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, 2Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 3Genetic Analysis Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 4Division of Psychiatric Genomics, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY 10029, 5Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 6Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 7Department of Genetics, Harvard Medical School, Boston, MA 02115 and 8Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27514, USA"}]},{"given":"Jared","family":"Maguire","sequence":"additional","affiliation":[{"name":"1 Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, 2Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 3Genetic Analysis Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 4Division of Psychiatric Genomics, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY 10029, 5Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 6Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 7Department of Genetics, Harvard Medical School, Boston, MA 02115 and 8Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27514, USA"}]},{"given":"Menachem","family":"Fromer","sequence":"additional","affiliation":[{"name":"1 Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, 2Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 3Genetic Analysis Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 4Division of Psychiatric Genomics, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY 10029, 5Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 6Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 7Department of Genetics, Harvard Medical School, Boston, MA 02115 and 8Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27514, USA"},{"name":"1 Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, 2Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 3Genetic Analysis Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 4Division of Psychiatric Genomics, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY 10029, 5Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 6Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 7Department of Genetics, Harvard Medical School, Boston, MA 02115 and 8Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27514, USA"},{"name":"1 Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, 2Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 3Genetic Analysis Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 4Division of Psychiatric Genomics, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY 10029, 5Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 6Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 7Department of Genetics, Harvard Medical School, Boston, MA 02115 and 8Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27514, USA"}]},{"given":"Colm","family":"O\u2019Dushlaine","sequence":"additional","affiliation":[{"name":"1 Analytical and Translational 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8Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27514, USA"},{"name":"1 Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, 2Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 3Genetic Analysis Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 4Division of Psychiatric Genomics, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY 10029, 5Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 6Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 7Department of Genetics, Harvard Medical School, Boston, MA 02115 and 8Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27514, USA"},{"name":"1 Analytical and Translational 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4Division of Psychiatric Genomics, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY 10029, 5Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 6Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 7Department of Genetics, Harvard Medical School, Boston, MA 02115 and 8Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27514, USA"}]},{"given":"Benjamin M.","family":"Neale","sequence":"additional","affiliation":[{"name":"1 Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, 2Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 3Genetic Analysis Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, 4Division of Psychiatric Genomics, Department of Psychiatry, Mount Sinai School 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