Introduction

ADTEx is a freely available software package coded using R statistical language and Python to detect somatic copy number variations (CNVs) and genotypes in tumour whole exome samples. ADTEx is suitable for paired tumour/matched normal samples. The overall algorithm consists of few steps including,

1. Calculate depth of coverage (DOC) ratios and B allele frequencies (BAFs)
2. Noise reduction in ratios
3. Apply first HMM to predict CNVs
4. Select heterozygous SNP loci in normal sample
5. Apply second HMM to predict genotypes

Availability

Source code, supporting files and user manual are freely available under GNU General Public License version 3.0 (GPLv3) for download for academic and non-profit use. A complete tutorial can be found here.

Installing ADTEx

Operating System

Linux

Requirements

1. R statistical language (R2.15)
   http://www.r-project.org/
2. wmtsa R package
   http://cran.r-project.org/web/packages/wmtsa/index.html
3. DNAcopy R package
   http://www.bioconductor.org/packages/release/bioc/html/DNAcopy.html
4. Python 2.7
   http://www.python.org/
5. BEDTools
   http://code.google.com/p/bedtools/