ADTEx

A tool for detection of copy number variation (CNV) in whole-genome exome data from paired or healthy tumor samples. The ADTex algorithm uses Hidden Markov Models (HMM) to predict CNV counts, genotypes, polyploidy, aneuploidy, cell contamination, and baseline shifts. The authors originally named ADTex to CoNVEX, but they changed the name because of the conflict with another tool.

Topic

Genetics;sequencing;oncology;Exome sequencing

Detail

  • Operation: Statistical calculation;variation detection

  • Software interface: Command-line user interface

  • Language: Python;R

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 2.0

  • Credit: Australian Research Council (grant DP1096296). KCA was funded by The University of Melbourne MIFRS and MIRS scholarships.

  • Input: BAM, BED

  • Output: -

  • Contact: kaushalyac@gmail.com

  • Collection: -

  • Maturity: Mature

Publications

  • CoNVEX: copy number variation estimation in exome sequencing data using HMM.
  • Amarasinghe KC, et al. CoNVEX: copy number variation estimation in exome sequencing data using HMM. CoNVEX: copy number variation estimation in exome sequencing data using HMM. 2013; 14 Suppl 2:S2. doi: 10.1186/1471-2105-14-S2-S2
  • https://doi.org/10.1186/1471-2105-14-S2-S2
  • PMID: 23368785
  • PMC: PMC3549847
  • Erratum to: CoNVEX: copy number variation estimation in exome sequencing data using HMM
  • Kaushik A, et al. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. 2015; 3:e1332. doi: 10.7717/peerj.1332
  • https://doi.org/10.1186/1471-2105-14-S2-S26
  • PMID: -
  • PMC: -
  • Inferring copy number and genotype in tumour exome data.
  • Amarasinghe KC, et al. Inferring copy number and genotype in tumour exome data. Inferring copy number and genotype in tumour exome data. 2014; 15:732. doi: 10.1186/1471-2164-15-732
  • https://doi.org/10.1186/1471-2164-15-732
  • PMID: 25167919
  • PMC: PMC4162913

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