ADTEx: Aberration Detection in Tumour Exome

Tutorial | Summary | Download | FAQ


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


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

Download ADTEx tarball and decompress it with the following command:
    tar -xvzf ADTEx.<version>.tar.gz

Operating System



  1. R statistical language (R2.15)
  2. wmtsa R package
  3. DNAcopy R package
  4. Python 2.7
  5. BEDTools
For support, queries and feedback, email to kaushalyac at gmail dot com

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