Literature DB >> 25431634

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

Geraldine A Van der Auwera1, Mauricio O Carneiro1, Christopher Hartl1, Ryan Poplin1, Guillermo Del Angel1, Ami Levy-Moonshine1, Tadeusz Jordan1, Khalid Shakir1, David Roazen1, Joel Thibault1, Eric Banks1, Kiran V Garimella2, David Altshuler1, Stacey Gabriel1, Mark A DePristo1.   

Abstract

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.

Entities:  

Keywords:  NGS; WGS; exome; genotyping; variant detection

Mesh：

Year:  2013        PMID： 25431634      PMCID： PMC4243306          DOI： 10.1002/0471250953.bi1110s43

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN： 1934-3396


  8 in total

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2.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

Authors:  Aaron McKenna; Matthew Hanna; Eric Banks; Andrey Sivachenko; Kristian Cibulskis; Andrew Kernytsky; Kiran Garimella; David Altshuler; Stacey Gabriel; Mark Daly; Mark A DePristo
Journal:  Genome Res       Date:  2010-07-19       Impact factor: 9.043

3.  Integrating common and rare genetic variation in diverse human populations.

Authors:  David M Altshuler; Richard A Gibbs; Leena Peltonen; David M Altshuler; Richard A Gibbs; Leena Peltonen; Emmanouil Dermitzakis; Stephen F Schaffner; Fuli Yu; Leena Peltonen; Emmanouil Dermitzakis; Penelope E Bonnen; David M Altshuler; Richard A Gibbs; Paul I W de Bakker; Panos Deloukas; Stacey B Gabriel; Rhian Gwilliam; Sarah Hunt; Michael Inouye; Xiaoming Jia; Aarno Palotie; Melissa Parkin; Pamela Whittaker; Fuli Yu; Kyle Chang; Alicia Hawes; Lora R Lewis; Yanru Ren; David Wheeler; Richard A Gibbs; Donna Marie Muzny; Chris Barnes; Katayoon Darvishi; Matthew Hurles; Joshua M Korn; Kati Kristiansson; Charles Lee; Steven A McCarrol; James Nemesh; Emmanouil Dermitzakis; Alon Keinan; Stephen B Montgomery; Samuela Pollack; Alkes L Price; Nicole Soranzo; Penelope E Bonnen; Richard A Gibbs; Claudia Gonzaga-Jauregui; Alon Keinan; Alkes L Price; Fuli Yu; Verneri Anttila; Wendy Brodeur; Mark J Daly; Stephen Leslie; Gil McVean; Loukas Moutsianas; Huy Nguyen; Stephen F Schaffner; Qingrun Zhang; Mohammed J R Ghori; Ralph McGinnis; William McLaren; Samuela Pollack; Alkes L Price; Stephen F Schaffner; Fumihiko Takeuchi; Sharon R Grossman; Ilya Shlyakhter; Elizabeth B Hostetter; Pardis C Sabeti; Clement A Adebamowo; Morris W Foster; Deborah R Gordon; Julio Licinio; Maria Cristina Manca; Patricia A Marshall; Ichiro Matsuda; Duncan Ngare; Vivian Ota Wang; Deepa Reddy; Charles N Rotimi; Charmaine D Royal; Richard R Sharp; Changqing Zeng; Lisa D Brooks; Jean E McEwen
Journal:  Nature       Date:  2010-09-02       Impact factor: 49.962

4.  An initial map of insertion and deletion (INDEL) variation in the human genome.

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Journal:  Genome Res       Date:  2006-08-10       Impact factor: 9.043

5.  A map of human genome variation from population-scale sequencing.

Authors:  Gonçalo R Abecasis; David Altshuler; Adam Auton; Lisa D Brooks; Richard M Durbin; Richard A Gibbs; Matt E Hurles; Gil A McVean
Journal:  Nature       Date:  2010-10-28       Impact factor: 49.962

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Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

7.  A framework for variation discovery and genotyping using next-generation DNA sequencing data.

Authors:  Mark A DePristo; Eric Banks; Ryan Poplin; Kiran V Garimella; Jared R Maguire; Christopher Hartl; Anthony A Philippakis; Guillermo del Angel; Manuel A Rivas; Matt Hanna; Aaron McKenna; Tim J Fennell; Andrew M Kernytsky; Andrey Y Sivachenko; Kristian Cibulskis; Stacey B Gabriel; David Altshuler; Mark J Daly
Journal:  Nat Genet       Date:  2011-04-10       Impact factor: 38.330

8.  Fast and accurate long-read alignment with Burrows-Wheeler transform.

Authors:  Heng Li; Richard Durbin
Journal:  Bioinformatics       Date:  2010-01-15       Impact factor: 6.937
  8 in total
  2000 in total

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Journal:  Am J Hum Genet       Date:  2017-08-03       Impact factor: 11.025

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Authors:  Maarten P G Massink; Marijn A Créton; Francesca Spanevello; Willem M M Fennis; Marco S Cune; Sanne M C Savelberg; Isaäc J Nijman; Madelon M Maurice; Marie-José H van den Boogaard; Gijs van Haaften
Journal:  Am J Hum Genet       Date:  2015-09-17       Impact factor: 11.025

5.  Tools and best practices for data processing in allelic expression analysis.

Authors:  Stephane E Castel; Ami Levy-Moonshine; Pejman Mohammadi; Eric Banks; Tuuli Lappalainen
Journal:  Genome Biol       Date:  2015-09-17       Impact factor: 13.583

6.  Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing.

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Journal:  Proc Natl Acad Sci U S A       Date:  2016-08-29       Impact factor: 11.205

7.  Genetic Polymorphisms in the Long Noncoding RNA MIR2052HG Offer a Pharmacogenomic Basis for the Response of Breast Cancer Patients to Aromatase Inhibitor Therapy.

Authors:  James N Ingle; Fang Xie; Matthew J Ellis; Paul E Goss; Lois E Shepherd; Judith-Anne W Chapman; Bingshu E Chen; Michiaki Kubo; Yoichi Furukawa; Yukihide Momozawa; Vered Stearns; Kathleen I Pritchard; Poulami Barman; Erin E Carlson; Matthew P Goetz; Richard M Weinshilboum; Krishna R Kalari; Liewei Wang
Journal:  Cancer Res       Date:  2016-10-10       Impact factor: 12.701

8.  Whole genome sequencing predicts novel human disease models in rhesus macaques.

Authors:  Benjamin N Bimber; Ranjani Ramakrishnan; Rita Cervera-Juanes; Ravi Madhira; Samuel M Peterson; Robert B Norgren; Betsy Ferguson
Journal:  Genomics       Date:  2017-04-23       Impact factor: 5.736

9.  Inactivation of Transcriptional Regulators during Within-Household Evolution of Escherichia coli.

Authors:  Dagmara I Kisiela; Matthew Radey; Sandip Paul; Stephen Porter; Kseniya Polukhina; Veronika Tchesnokova; Sofiya Shevchenko; Diana Chan; Maliha Aziz; Timothy J Johnson; Lance B Price; James R Johnson; Evgeni V Sokurenko
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