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
Download and documentation
Source: https://sourceforge.net/projects/adtex/files/ADTEx.v2.0/
Documentation: https://sourceforge.net/projects/adtex/files/User%20Guide/
Home page: http://adtex.sourceforge.net/
Data: https://sourceforge.net/projects/adtex/files/Test%20Data/
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