Zcall: A rare variant caller for array-based genotyping

Jacqueline I. Goldstein; Andrew Crenshaw; Jason Carey; George B. Grant; Jared Maguire; Menachem Fromer; Colm O'dushlaine; Jennifer L. Moran; Kimberly Chambert; Christine Stevens; Pamela Sklar; Christina M. Hultman; Shaun Purcell; Steven A. Mccarroll; Patrick F. Sullivan; Mark J. Daly; Benjamin M. Neale

doi:10.1093/bioinformatics/bts479

Zcall: A rare variant caller for array-based genotyping

Jacqueline I. Goldstein
, Andrew Crenshaw
, Jason Carey
, George B. Grant
, Jared Maguire
, Menachem Fromer
, Colm O'dushlaine
, Jennifer L. Moran
, Kimberly Chambert
, Christine Stevens
, Pamela Sklar
, Christina M. Hultman
, Shaun Purcell
, Steven A. Mccarroll
, Patrick F. Sullivan
, Mark J. Daly
, Benjamin M. Neale

Research output: Contribution to journal › Article › peer-review

167 Scopus citations

Abstract

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.

Original language	English
Article number	bts479
Pages (from-to)	2543-2545
Number of pages	3
Journal	Bioinformatics
Volume	28
Issue number	19
DOIs	https://doi.org/10.1093/bioinformatics/bts479
State	Published - Oct 2012
Externally published	Yes

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Goldstein, J. I., Crenshaw, A., Carey, J., Grant, G. B., Maguire, J., Fromer, M., O'dushlaine, C., Moran, J. L., Chambert, K., Stevens, C., Sklar, P., Hultman, C. M., Purcell, S., Mccarroll, S. A., Sullivan, P. F., Daly, M. J., & Neale, B. M. (2012). Zcall: A rare variant caller for array-based genotyping. Bioinformatics, 28(19), 2543-2545. Article bts479. https://doi.org/10.1093/bioinformatics/bts479

@article{11b01afa0c9045adb7684f4267c3c7ac,

title = "Zcall: A rare variant caller for array-based genotyping",

abstract = "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.",

author = "Goldstein, \{Jacqueline I.\} and Andrew Crenshaw and Jason Carey and Grant, \{George B.\} and Jared Maguire and Menachem Fromer and Colm O'dushlaine and Moran, \{Jennifer L.\} and Kimberly Chambert and Christine Stevens and Pamela Sklar and Hultman, \{Christina M.\} and Shaun Purcell and Mccarroll, \{Steven A.\} and Sullivan, \{Patrick F.\} and Daly, \{Mark J.\} and Neale, \{Benjamin M.\}",

year = "2012",

month = oct,

doi = "10.1093/bioinformatics/bts479",

language = "English",

volume = "28",

pages = "2543--2545",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "19",

}

Goldstein, JI, Crenshaw, A, Carey, J, Grant, GB, Maguire, J, Fromer, M, O'dushlaine, C, Moran, JL, Chambert, K, Stevens, C, Sklar, P, Hultman, CM, Purcell, S, Mccarroll, SA, Sullivan, PF, Daly, MJ & Neale, BM 2012, 'Zcall: A rare variant caller for array-based genotyping', Bioinformatics, vol. 28, no. 19, bts479, pp. 2543-2545. https://doi.org/10.1093/bioinformatics/bts479

TY - JOUR

T1 - Zcall

T2 - A rare variant caller for array-based genotyping

AU - Goldstein, Jacqueline I.

AU - Crenshaw, Andrew

AU - Carey, Jason

AU - Grant, George B.

AU - Maguire, Jared

AU - Fromer, Menachem

AU - O'dushlaine, Colm

AU - Moran, Jennifer L.

AU - Chambert, Kimberly

AU - Stevens, Christine

AU - Sklar, Pamela

AU - Hultman, Christina M.

AU - Purcell, Shaun

AU - Mccarroll, Steven A.

AU - Sullivan, Patrick F.

AU - Daly, Mark J.

AU - Neale, Benjamin M.

PY - 2012/10

Y1 - 2012/10

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/84867293769

U2 - 10.1093/bioinformatics/bts479

DO - 10.1093/bioinformatics/bts479

M3 - Article

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AN - SCOPUS:84867293769

SN - 1367-4803

VL - 28

SP - 2543

EP - 2545

JO - Bioinformatics

JF - Bioinformatics

IS - 19

M1 - bts479

ER -

Zcall: A rare variant caller for array-based genotyping

Abstract

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