zCall: a rare variant caller for array-based genotyping

被引：149

作者：

Goldstein, Jacqueline I. ^{[1
,2
,3
]}

Crenshaw, Andrew

Carey, Jason

Grant, George B.

Maguire, Jared ^{[3
]}

Fromer, Menachem ^{[1
,2
,3
,4
]}

O'Dushlaine, Colm ^{[5
]}

Moran, Jennifer L. ^{[5
]}

Chambert, Kimberly ^{[5
]}

Stevens, Christine ^{[3
]}

Sklar, Pamela ^{[4
]}

Hultman, Christina M. ^{[6
]}

Purcell, Shaun ^{[1
,2
,4
,5
]}

McCarroll, Steven A. ^{[3
,5
,7
]}

Sullivan, Patrick F. ^{[8
]}

Daly, Mark J. ^{[1
,2
,3
]}

Neale, Benjamin M. ^{[1
,2
,3
,5
]}

机构：

[1] Massachusetts Gen Hosp, Dept Med, Analyt & Translat Genet Unit, Boston, MA 02114 USA

[2] Harvard Univ, Sch Med, Boston, MA 02114 USA

[3] Broad Inst MIT & Harvard, Program Med & Populat Genet, Cambridge, MA 02142 USA

[4] Mt Sinai Sch Med, Dept Psychiat, Div Psychiat Genom, New York, NY 10029 USA

[5] Broad Inst MIT & Harvard, Stanley Ctr Psychiat Res, Cambridge, MA 02142 USA

[6] Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden

[7] Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA

[8] Univ N Carolina, Chapel Hill Sch Med, Dept Genet, Chapel Hill, NC 27514 USA

来源：

BIOINFORMATICS | 2012年 / 28卷 / 19期

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1093/bioinformatics/bts479

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2543 / 2545

页数：3

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