Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

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Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

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Title: Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls
Author: Zook, Justin M; Chapman, Brad Alan; Wang, Jason; Mittelman, David; Hofmann, Oliver Marc; Hide, Winston; Salit, Marc

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Citation: Zook, Justin M, Brad Chapman, Jason Wang, David Mittelman, Oliver Hofmann, Winston Hide, and Marc Salit. 2014. “Integrating Human Sequence Data Sets Provides a Resource of Benchmark SNP and Indel Genotype Calls.” Nature Biotechnology 32 (3) (February 16): 246–251.
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Abstract: Clinical adoption of human genome sequencing requires methods that output genotypes with known accuracy at millions or billions of positions across a genome. Because of substantial discordance among calls made by existing sequencing methods and algorithms, there is a need for a highly accurate set of genotypes across a genome that can be used as a benchmark. Here we present methods to make high-confidence, single-nucleotide polymorphism (SNP), indel and homozygous reference genotype calls for NA12878, the pilot genome for the Genome in a Bottle Consortium. We minimize bias toward any method by integrating and arbitrating between 14 data sets from five sequencing technologies, seven read mappers and three variant callers. We identify regions for which no confident genotype call could be made, and classify them into different categories based on reasons for uncertainty. Our genotype calls are publicly available on the Genome Comparison and Analytic Testing website to enable real-time benchmarking of any method.
Published Version: doi:10.1038/nbt.2835
Terms of Use: This article is made available under the terms and conditions applicable to Open Access Policy Articles, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#OAP
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:12561353
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