zCall: a rare variant caller for array-based genotyping
Open accessAbstract
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. Availability: http://atguweb.mgh.harvard.edu/apps/zcall. Contact: bneale@broadinstitute.org Supplementary Information: Supplementary data are available at Bioinformatics online.
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- Authors
- Goldstein, J. I., Crenshaw, A., Carey, J., Grant, G. B., Maguire, J., Fromer, M., O’Dushlaine, C., Moran, J. L., Chambert, K., Stevens, C., Swedish Schizophrenia Consortium, ARRA Autism Sequencing Consortium, Sklar, P., Hultman, C. M., Purcell, S., McCarroll, S. A., Sullivan, P. F., Daly, M. J., & Neale, B. M.
- Affiliations
- Broad Institute (US)
- Corresponding author
- Neale, Benjamin M.
- ORCID
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-07-27
- Volume
- 28
- Issue
- 19
- Pages
- 2543-2545
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC3463112
- OpenAlex
- W2098510019
- Cited by
- 196
- References
- 7
- Citations by year
- 2026: 2 · 2025: 7 · 2024: 5 · 2023: 16 · 2022: 12 · 2021: 11 · 2020: 12 · 2019: 18 · 2018: 17 · 2017: 27 · 2016: 22 · 2015: 20 · 2014: 21 · 2013: 6
- FWCI
- 9.06
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
- UNC Libraries
- Funders
- Stanley Medical Research Institute
- Gerstner Family Foundation
- Broad Institute
- Forskningsrådet för Arbetsliv och Socialvetenskap (2001-2368)
- National Institutes of Health
- National Institute of Mental Health (R01MH089025, MH089004, MH089025, R01MH089175, MH089175, MH089208, R01MH089004, R01MH089208, MH089482, R01MH095034, R01MH089482, MH079126)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- single nucleotide polymorphisms, array-based genotyping, exome sequencing
- MeSH terms
- Algorithms, Alleles, Homozygote, Humans, Software, Cluster Analysis, Polymorphism, Single Nucleotide, Exome, Genotyping Techniques
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