title: The distribution and mutagenesis of short coding INDELs from 1,128 whole exomes.
abstract: BACKGROUND
  Identifying insertion/deletion polymorphisms (INDELs) with high confidence has been intrinsically challenging in short-read sequencing data. Here we report our approach for improving INDEL calling accuracy by using a machine learning algorithm to combine call sets generated with three independent methods, and by leveraging the strengths of each individual pipeline. Utilizing this approach, we generated a consensus exome INDEL call set from a large dataset generated by the 1000 Genomes Project (1000G), maximizing both the sensitivity and the specificity of the calls.
  
  
  RESULTS
  This consensus exome INDEL call set features 7,210 INDELs, from 1,128 individuals across 13 populations included in the 1000 Genomes Phase 1 dataset, with a false discovery rate (FDR) of about 7.0%.
  
  
  CONCLUSIONS
  In our study we further characterize the patterns and distributions of these exonic INDELs with respect to density, allele length, and site frequency spectrum, as well as the potential mutagenic mechanisms of coding INDELs in humans.
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA. dannychallis@gmail.com.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. dannychallis@gmail.com.|Present address: Monsanto Company, Ankeny, IA, 50021, USA. dannychallis@gmail.com.
authors.forename: Danny
authors.initials: D
authors.lastname: Challis
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA. lilian.antunes@gmail.com.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. lilian.antunes@gmail.com.|Present address: Washington University School of Medicine, Saint Louis, MO, 63110, USA. lilian.antunes@gmail.com.
authors.forename: Lilian
authors.initials: L
authors.lastname: Antunes
authors.affiliation: Department of Biology, Boston College, Wellcome Trust Sanger Institute, Chestnut Hill, MA, 02467, USA. erik.garrison@bc.edu.
authors.forename: Erik
authors.initials: E
authors.lastname: Garrison
authors.affiliation: Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. ebanks@broadinstitute.org.
authors.forename: Eric
authors.initials: E
authors.lastname: Banks
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA. udayevani@gmail.com.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. udayevani@gmail.com.|Present address: New York Genome Center, New York, NY, 10013, USA. udayevani@gmail.com.
authors.forename: Uday S
authors.initials: US
authors.lastname: Evani
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA. donnam@bcm.edu.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. donnam@bcm.edu.
authors.forename: Donna
authors.initials: D
authors.lastname: Muzny
authors.affiliation: Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. rpoplin@broadinstitute.org.
authors.forename: Ryan
authors.initials: R
authors.lastname: Poplin
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA. agibbs@bcm.edu.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. agibbs@bcm.edu.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Gibbs
authors.affiliation: Department of Biology, Boston College, Wellcome Trust Sanger Institute, Chestnut Hill, MA, 02467, USA. marth@bc.edu.|Present address: Department of Human Genetics and Utah Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA. marth@bc.edu.
authors.forename: Gabor
authors.initials: G
authors.lastname: Marth
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA. fyu@bcm.edu.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. fyu@bcm.edu.|Institute of Neurology, Tianjin Medical University General Hospital, Tianjin, 300052, China. fyu@bcm.edu.
authors.forename: Fuli
authors.initials: F
authors.lastname: Yu
mesh_terms: D019295:Computational Biology; D059472:Exome / Q000235:genetics*; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D016045:Human Genome Project; D006801:Humans; D054643:INDEL Mutation / Q000235:genetics*; D000069550:Machine Learning; D016296:Mutagenesis