From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.

Van der Auwera, Geraldine A; Carneiro, Mauricio O; Hartl, Christopher; Poplin, Ryan; Del Angel, Guillermo; Levy-Moonshine, Ami; Jordan, Tadeusz; Shakir, Khalid; Roazen, David; Thibault, Joel; Banks, Eric; Garimella, Kiran V; Altshuler, David; Gabriel, Stacey; DePristo, Mark A

Van der Auwera, Geraldine A; Carneiro, Mauricio O; Hartl, Christopher; Poplin, Ryan; Del Angel, Guillermo; Levy-Moonshine, Ami; Jordan, Tadeusz; Shakir, Khalid; Roazen, David; Thibault, Joel; Banks, Eric; Garimella, Kiran V; Altshuler, David; Gabriel, Stacey; DePristo, Mark A.

Afiliación

Van der Auwera GA; Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
Carneiro MO; Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
Hartl C; Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
Poplin R; Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
Del Angel G; Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
Levy-Moonshine A; Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
Jordan T; Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
Shakir K; Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
Roazen D; Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
Thibault J; Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
Banks E; Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
Garimella KV; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
Altshuler D; Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
Gabriel S; Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
DePristo MA; Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.

Curr Protoc Bioinformatics ; 43: 11.10.1-11.10.33, 2013.

Article en En | MEDLINE | ID: mdl-25431634

RESUMEN

This unit describes how to use BWA and the Genome Analysis Toolkit (GATK) to map genome sequencing data to a reference and produce high-quality variant calls that can be used in downstream analyses. The complete workflow includes the core NGS data processing steps that are necessary to make the raw data suitable for analysis by the GATK, as well as the key methods involved in variant discovery using the GATK.

Asunto(s)

Variación Genética; Genoma Humano; Programas Informáticos; Calibración; Bases de Datos Genéticas; Haploidia; Haplotipos/genética; Humanos; Anotación de Secuencia Molecular; Polimorfismo de Nucleótido Simple/genética; Alineación de Secuencia

Palabras clave

NGS; WGS; exome; genotyping; variant detection

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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Variación Genética / Programas Informáticos / Genoma Humano Tipo de estudio: Guideline Límite: Humans Idioma: En Revista: Curr Protoc Bioinformatics Año: 2013 Tipo del documento: Article

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