title: Consensus Genotyper for Exome Sequencing (CGES): improving the quality of exome variant genotypes.
abstract: BACKGROUND
  The development of cost-effective next-generation sequencing methods has spurred the development of high-throughput bioinformatics tools for detection of sequence variation. With many disparate variant-calling algorithms available, investigators must ask, 'Which method is best for my data?' Machine learning research has shown that so-called ensemble methods that combine the output of multiple models can dramatically improve classifier performance. Here we describe a novel variant-calling approach based on an ensemble of variant-calling algorithms, which we term the Consensus Genotyper for Exome Sequencing (CGES). CGES uses a two-stage voting scheme among four algorithm implementations. While our ensemble method can accept variants generated by any variant-calling algorithm, we used GATK2.8, SAMtools, FreeBayes and Atlas-SNP2 in building CGES because of their performance, widespread adoption and diverse but complementary algorithms.
  
  
  RESULTS
  We apply CGES to 132 samples sequenced at the Hudson Alpha Institute for Biotechnology (HAIB, Huntsville, AL) using the Nimblegen Exome Capture and Illumina sequencing technology. Our sample set consisted of 40 complete trios, two families of four, one parent-child duo and two unrelated individuals. CGES yielded the fewest total variant calls (N(CGES) = 139° 897), the highest Ts/Tv ratio (3.02), the lowest Mendelian error rate across all genotypes (0.028%), the highest rediscovery rate from the Exome Variant Server (EVS; 89.3%) and 1000 Genomes (1KG; 84.1%) and the highest positive predictive value (PPV; 96.1%) for a random sample of previously validated de novo variants. We describe these and other quality control (QC) metrics from consensus data and explain how the CGES pipeline can be used to generate call sets of varying quality stringency, including consensus calls present across all four algorithms, calls that are consistent across any three out of four algorithms, calls that are consistent across any two out of four algorithms or a more liberal set of all calls made by any algorithm.
  
  
  METHODS
  To enable accessible, efficient and reproducible analysis, we implement CGES both as a stand-alone command line tool available for download in GitHub and as a set of Galaxy tools and workflows configured to execute on parallel computers.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Medicine, Section of Genetic Medicine, Computation Institute, University of Chicago, Chicago, IL 60637, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, USA, Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN 37232 and Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA.
authors.forename: Vassily
authors.initials: V
authors.lastname: Trubetskoy
authors.affiliation: Department of Medicine, Section of Genetic Medicine, Computation Institute, University of Chicago, Chicago, IL 60637, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, USA, Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN 37232 and Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Rodriguez
authors.affiliation: Department of Medicine, Section of Genetic Medicine, Computation Institute, University of Chicago, Chicago, IL 60637, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, USA, Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN 37232 and Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA.
authors.forename: Uptal
authors.initials: U
authors.lastname: Dave
authors.affiliation: Department of Medicine, Section of Genetic Medicine, Computation Institute, University of Chicago, Chicago, IL 60637, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, USA, Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN 37232 and Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA Department of Medicine, Section of Genetic Medicine, Computation Institute, University of Chicago, Chicago, IL 60637, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, USA, Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN 37232 and Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Campbell
authors.affiliation: Department of Medicine, Section of Genetic Medicine, Computation Institute, University of Chicago, Chicago, IL 60637, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, USA, Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN 37232 and Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA Department of Medicine, Section of Genetic Medicine, Computation Institute, University of Chicago, Chicago, IL 60637, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, USA, Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN 37232 and Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA.
authors.forename: Emily L
authors.initials: EL
authors.lastname: Crawford
authors.affiliation: Department of Medicine, Section of Genetic Medicine, Computation Institute, University of Chicago, Chicago, IL 60637, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, USA, Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN 37232 and Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA.
authors.forename: Edwin H
authors.initials: EH
authors.lastname: Cook
authors.affiliation: Department of Medicine, Section of Genetic Medicine, Computation Institute, University of Chicago, Chicago, IL 60637, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, USA, Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN 37232 and Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA Department of Medicine, Section of Genetic Medicine, Computation Institute, University of Chicago, Chicago, IL 60637, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, USA, Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN 37232 and Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA.
authors.forename: James S
authors.initials: JS
authors.lastname: Sutcliffe
authors.affiliation: Department of Medicine, Section of Genetic Medicine, Computation Institute, University of Chicago, Chicago, IL 60637, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, USA, Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN 37232 and Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA.
authors.forename: Ian
authors.initials: I
authors.lastname: Foster
authors.affiliation: Department of Medicine, Section of Genetic Medicine, Computation Institute, University of Chicago, Chicago, IL 60637, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, USA, Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN 37232 and Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA.
authors.forename: Ravi
authors.initials: R
authors.lastname: Madduri
authors.affiliation: Department of Medicine, Section of Genetic Medicine, Computation Institute, University of Chicago, Chicago, IL 60637, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, USA, Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN 37232 and Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA.
authors.forename: Nancy J
authors.initials: NJ
authors.lastname: Cox
authors.affiliation: Department of Medicine, Section of Genetic Medicine, Computation Institute, University of Chicago, Chicago, IL 60637, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, USA, Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN 37232 and Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA.
authors.forename: Lea K
authors.initials: LK
authors.lastname: Davis
mesh_terms: D000465:Algorithms; D001321:Autistic Disorder / Q000235:genetics*; D016384:Consensus Sequence; D003627:Data Interpretation, Statistical; D059472:Exome / Q000235:genetics*; D005820:Genetic Testing; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012984:Software