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Bioinformatics. 2012 Oct 1;28(19):2543-5. Epub 2012 Jul 27.

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

Author information

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

Abstract

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.

PMID:
22843986
[PubMed - indexed for MEDLINE]
PMCID:
PMC3463112
Free PMC Article

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