title: RVD: a command-line program for ultrasensitive rare single nucleotide variant detection using targeted next-generation DNA resequencing.
abstract: BACKGROUND
  Rare single nucleotide variants play an important role in genetic diversity and heterogeneity of specific human disease. For example, an individual clinical sample can harbor rare mutations at minor frequencies. Genetic diversity within an individual clinical sample is oftentimes reflected in rare mutations. Therefore, detecting rare variants prior to treatment may prove to be a useful predictor for therapeutic response. Current rare variant detection algorithms using next generation DNA sequencing are limited by inherent sequencing error rate and platform availability.
  
  
  RESULTS
  Here we describe an optimized implementation of a rare variant detection algorithm called RVD for use in targeted gene resequencing. RVD is available both as a command-line program and for use in MATLAB and estimates context-specific error using a beta-binomial model to call variants with minor allele frequency (MAF) as low as 0.1%. We show that RVD accepts standard BAM formatted sequence files. We tested RVD analysis on multiple Illumina sequencing platforms, among the most widely used DNA sequencing platforms.
  
  
  CONCLUSIONS
  RVD meets a growing need for highly sensitive and specific tools for variant detection. To demonstrate the usefulness of RVD, we carried out a thorough analysis of the software's performance on synthetic and clinical virus samples sequenced on both an Illumina GAIIx and a MiSeq. We expect RVD can improve understanding the genetics and treatment of common viral diseases including influenza. RVD is available at the following URL:http://dna-discovery.stanford.edu/software/rvd/.
authors.affiliation: Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA. genomics_ji@stanford.edu.
authors.forename: Anna
authors.initials: A
authors.lastname: Cushing
authors.forename: Patrick
authors.initials: P
authors.lastname: Flaherty
authors.forename: Erik
authors.initials: E
authors.lastname: Hopmans
authors.forename: John M
authors.initials: JM
authors.lastname: Bell
authors.forename: Hanlee P
authors.initials: HP
authors.lastname: Ji
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D057230:Limit of Detection; D009711:Nucleotides / Q000737:chemistry*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D009711:Nucleotides