zCall: a rare variant caller for array-based genotyping: genetics and population analysis
Jacqueline I Goldstein, Andrew Crenshaw, Jason Carey, George B Grant, Jared Maguire, Menachem Fromer, Colm O'Dushlaine, Jennifer L Moran, Kimberly Chambert, Christine Stevens, Swedish Schizophrenia Consortium, ARRA Autism Sequencing Consortium, Pamela Sklar, Christina M Hultman, Shaun Purcell, Steven A McCarroll, Patrick F Sullivan, Mark J Daly, Benjamin M Neale, Jacqueline I Goldstein, Andrew Crenshaw, Jason Carey, George B Grant, Jared Maguire, Menachem Fromer, Colm O'Dushlaine, Jennifer L Moran, Kimberly Chambert, Christine Stevens, Swedish Schizophrenia Consortium, ARRA Autism Sequencing Consortium, Pamela Sklar, Christina M Hultman, Shaun Purcell, Steven A McCarroll, Patrick F Sullivan, Mark J Daly, Benjamin M Neale
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.
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Source: PubMed