title: Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications.
abstract: High-throughput DNA sequencing technology has transformed genetic research and is starting to make an impact on clinical practice. However, analyzing high-throughput sequencing data remains challenging, particularly in clinical settings where accuracy and turnaround times are critical. We present a new approach to this problem, implemented in a software package called Platypus. Platypus achieves high sensitivity and specificity for SNPs, indels and complex polymorphisms by using local de novo assembly to generate candidate variants, followed by local realignment and probabilistic haplotype estimation. It is an order of magnitude faster than existing tools and generates calls from raw aligned read data without preprocessing. We demonstrate the performance of Platypus in clinically relevant experimental designs by comparing with SAMtools and GATK on whole-genome and exome-capture data, by identifying de novo variation in 15 parent-offspring trios with high sensitivity and specificity, and by estimating human leukocyte antigen genotypes directly from variant calls.
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
authors.forename: Andy
authors.initials: A
authors.lastname: Rimmer
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
authors.forename: Hang
authors.initials: H
authors.lastname: Phan
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
authors.forename: Iain
authors.initials: I
authors.lastname: Mathieson
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
authors.forename: Zamin
authors.initials: Z
authors.lastname: Iqbal
authors.affiliation: Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK.
authors.forename: Stephen R F
authors.initials: SRF
authors.lastname: Twigg
authors.affiliation: Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK.
authors.forename: Andrew O M
authors.initials: AOM
authors.lastname: Wilkie
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.|Department of Statistics, University of Oxford, Oxford, UK.
authors.forename: Gil
authors.initials: G
authors.lastname: McVean
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
authors.forename: Gerton
authors.initials: G
authors.lastname: Lunter
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D059472:Exome; D015894:Genome, Human; D056914:Genomic Structural Variation; D005838:Genotype; D006680:HLA Antigens / Q000235:genetics; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D006680:HLA Antigens