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zCall: a rare variant caller for array-based genotyping: genetics and population analysis.

Jacqueline I Goldstein¹, Andrew Crenshaw, Jason Carey

¹Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.

Bioinformatics (Oxford, England)

|July 31, 2012

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zCall improves the detection of rare single-nucleotide polymorphisms (SNPs) using array-based technology. This variant caller enhances rare allele identification when combined with exome sequencing data.

Area of Science:

Genetics
Bioinformatics

Background:

Array-based genotyping technologies are widely used for genetic studies.
Accurate calling of rare variants remains a challenge in genetic analysis.

Purpose of the Study:

To introduce zCall, a novel variant caller for rare single-nucleotide polymorphisms (SNPs).
To evaluate the performance of zCall as a post-processing step for array-based data.

Main Methods:

zCall utilizes the intensity profile of common allele homozygote clusters.
It defines the positions of other genotype clusters based on this profile.
The caller is applied after a default calling algorithm.

Main Results:

zCall demonstrated improved detection of rare alleles.

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Enhanced performance was observed when zCall was applied to data combining Illumina Infinium HumanExome BeadChip and exome sequencing.

Conclusions:

zCall is effective for calling rare SNPs from array-based data.
Integrating zCall with exome sequencing data improves rare variant detection.