RVD2: An ultra-sensitive variant detection model for low-depth targeted next-generation sequencing dataThis page contains supplemental data files and computer code for RVD2.
We provide a python module containing the core functionality of RVD2. This module depends on the following modules: numpy, scipy, itertools, h5py tempfile, logging, datetime, os, subprocess, re, pdb and time. To run in multithreaded mode, you also need the multiprocessing module.
RVD2 can be run as a command line program or imported into an existing python script as a module. Make the file executable and call
$ rvd27.py from the command line to print a usage message.
You'll need a small utility program to convert the pileup files to tab-deliminted depth chart format required by RVD2. Download the main.c program below and compile it to an executable using gcc.
The simulation data used for the experiment in the results section are provided at the following locations:
- Tumor and Normal data for HCC1187 was obtained from https://basespace.illumina.com/project/744744/TumorNormal_WGS_HiSeq2000_CSW_0-23 on 10/30/2013.
- Synthetic DNA data was obtained from http://dna-discovery.stanford.edu/software/rvd/ under the heading "Synthetic DNA Data"
We provide a demo to test if RVD2 CLI can be successfully run in your computer.
A success message will be displayed upon finish. Three hdf5 files and a vcf file will be created in the directory provided those should match these results: demo result files .