title: SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations.
abstract: Various approaches to calling single-nucleotide variants (SNVs) or insertion-or-deletion (indel) mutations have been developed based on next-generation sequencing (NGS). However, most of them are dedicated to a particular type of mutation, e.g. germline SNVs in normal cells, somatic SNVs in cancer/tumor cells, or indels only. In the literature, efficient and integrated callers for both germline and somatic SNVs/indels have not yet been extensively investigated.
  
  
  
  We present SNVSniffer, an efficient and integrated caller identifying both germline and somatic SNVs/indels from NGS data. In this algorithm, we propose the use of Bayesian probabilistic models to identify SNVs and investigate a multiple ungapped alignment approach to call indels. For germline variant calling, we model allele counts per site to follow a multinomial conditional distribution. For somatic variant calling, we rely on paired tumor-normal pairs from identical individuals and introduce a hybrid subtraction and joint sample analysis approach by modeling tumor-normal allele counts per site to follow a joint multinomial conditional distribution. A comprehensive performance evaluation has been conducted using a diversity of variant calling benchmarks. For germline variant calling, SNVSniffer demonstrates highly competitive accuracy with superior speed in comparison with the state-of-the-art FaSD, GATK and SAMtools. For somatic variant calling, our algorithm achieves comparable or even better accuracy, at fast speed, than the leading VarScan2, SomaticSniper, JointSNVMix2 and MuTect.
  
  
  
  SNVSniffers demonstrates the feasibility to develop integrated solutions to fast and efficient identification of germline and somatic variants. Nonetheless, accurate discovery of genetic variations is critical yet challenging, and still requires substantially more research efforts being devoted. SNVSniffer and synthetic samples are publicly available at http://snvsniffer.sourceforge.net .
authors.affiliation: School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, 30332, Georgia, USA. yliu@cc.gatech.edu.
authors.forename: Yongchao
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Translational Oncology, Johannes Gutenberg University Medical Center gGmbH Mainz, Mainz, 55131, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Loewer
authors.affiliation: School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, 30332, Georgia, USA.
authors.forename: Srinivas
authors.initials: S
authors.lastname: Aluru
authors.affiliation: Institute of Computer Science, Johannes Gutenberg University Mainz, Mainz, 55128, Germany.
authors.forename: Bertil
authors.initials: B
authors.lastname: Schmidt
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D018284:Cystadenocarcinoma, Serous / Q000235:genetics / Q000473:pathology; D005260:Female; D005787:Gene Frequency; D005854:Germ Cells / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D054643:INDEL Mutation; D010051:Ovarian Neoplasms / Q000235:genetics / Q000473:pathology; D020641:Polymorphism, Single Nucleotide
keywords: Bayesian model; Indel calling; SNP calling; Somatic SNV calling