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Bioinformatics DOI:10.1093/bioinformatics/bts479

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

Publication TypeJournal Article
Year of Publication2012
AuthorsGoldstein, 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
Corporate AuthorsSwedish Schizophrenia Consortium, ARRA Autism Sequencing Consortium
JournalBioinformatics
Volume28
Issue19
Pages2543-5
Date Published2012 Oct 01
ISSN1367-4811
KeywordsAlgorithms, Alleles, Cluster Analysis, Exome, Genotyping Techniques, Homozygote, Humans, Polymorphism, Single Nucleotide, Software
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.

URLhttp://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=22843986
DOI10.1093/bioinformatics/bts479
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/22843986?dopt=Abstract

Alternate JournalBioinformatics
PubMed ID22843986
PubMed Central IDPMC3463112
Grant ListR01 MH089208 / MH / NIMH NIH HHS / United States
R01 MH095034 / MH / NIMH NIH HHS / United States
MH089175 / MH / NIMH NIH HHS / United States
MH089208 / MH / NIMH NIH HHS / United States
R01 MH089004 / MH / NIMH NIH HHS / United States
MH089004 / MH / NIMH NIH HHS / United States
MH089025 / MH / NIMH NIH HHS / United States
R01 MH089025 / MH / NIMH NIH HHS / United States
R01 MH089175 / MH / NIMH NIH HHS / United States
MH079126 / MH / NIMH NIH HHS / United States
MH089482 / MH / NIMH NIH HHS / United States
R01 MH089482 / MH / NIMH NIH HHS / United States