title: A framework for variation discovery and genotyping using next-generation DNA sequencing data.
abstract: Recent advances in sequencing technology make it possible to comprehensively catalog genetic variation in population samples, creating a foundation for understanding human disease, ancestry and evolution. The amounts of raw data produced are prodigious, and many computational steps are required to translate this output into high-quality variant calls. We present a unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs. Our process includes (i) initial read mapping; (ii) local realignment around indels; (iii) base quality score recalibration; (iv) SNP discovery and genotyping to find all potential variants; and (v) machine learning to separate true segregating variation from machine artifacts common to next-generation sequencing technologies. We here discuss the application of these tools, instantiated in the Genome Analysis Toolkit, to deep whole-genome, whole-exome capture and multi-sample low-pass (∼4×) 1000 Genomes Project datasets.
authors.affiliation: Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. depristo@broadinstitute.org
authors.forename: Mark A
authors.initials: MA
authors.lastname: DePristo
authors.forename: Eric
authors.initials: E
authors.lastname: Banks
authors.forename: Ryan
authors.initials: R
authors.lastname: Poplin
authors.forename: Kiran V
authors.initials: KV
authors.lastname: Garimella
authors.forename: Jared R
authors.initials: JR
authors.lastname: Maguire
authors.forename: Christopher
authors.initials: C
authors.lastname: Hartl
authors.forename: Anthony A
authors.initials: AA
authors.lastname: Philippakis
authors.forename: Guillermo
authors.initials: G
authors.lastname: del Angel
authors.forename: Manuel A
authors.initials: MA
authors.lastname: Rivas
authors.forename: Matt
authors.initials: M
authors.lastname: Hanna
authors.forename: Aaron
authors.initials: A
authors.lastname: McKenna
authors.forename: Tim J
authors.initials: TJ
authors.lastname: Fennell
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Kernytsky
authors.forename: Andrey Y
authors.initials: AY
authors.lastname: Sivachenko
authors.forename: Kristian
authors.initials: K
authors.lastname: Cibulskis
authors.forename: Stacey B
authors.initials: SB
authors.lastname: Gabriel
authors.forename: David
authors.initials: D
authors.lastname: Altshuler
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Daly
mesh_terms: D003627:Data Interpretation, Statistical; D030561:Databases, Nucleic Acid; D005091:Exons; D014644:Genetic Variation; D005828:Genetics, Population / Q000379:methods / Q000706:statistics & numerical data; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment / Q000379:methods / Q000706:statistics & numerical data; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000706:statistics & numerical data; D012984:Software