Software

RVD: a command-line program for ultrasensitive rare single nucleotide variant detection using targeted next-generation DNA resequencing

INTRODUCTION

The RVD program takes BAM files of deep sequencing reads in as input. Using a Beta-Binomial model, the algorithm estimates the error rate at each base position in the reference sequence.

IMPLEMENTATION

Download User Guide (pdf)

AVAILABILITY

Executable binaries available for mac and 64-bit Linux:

Data files and computer code for RVD2 available here

CITATIONS

Cushing A, Flaherty P, Hopmans E, Bell JM, Ji HP. RVD: a command-line program for ultrasensitive rare single nucleotide variant detection using targeted next-generation DNA resequencing. BMC Res Notes. 2013; 6: 206.

Anna Cushing, Amanda Kamali, Mark Winters, Erik S. Hopmans,John M. Bell, Susan M. Grimes, Li C. Xia, Nancy R. Zhang, Ronald B. Moss, Mark Holodniy,Hanlee P. Ji. Emergence of Hemagglutinin Mutations During the Course of Influenza Infection. Sci Rep. 2015; 5: 16178.