ADTEx

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Application data

Created by Kaushalya Amarasinghe
Biological application domain(s) Copy number estimation, Next Generation Sequencing, Cancer biology, Exome analysis
Principal bioinformatics method(s) Statistical calculation
Technology Illumina
Created at The University of Melbourne
Maintained? Yes
Input format(s) BAM, BED
Output format(s) Tab-delimited file
Software features Copy number analysis
Programming language(s) Python, R
Interface type(s) Command line
Resource type(s) Command-line tool
Licence GPLv3
Operating system(s) GNU/Linux

Summary: Aberration Detection in Tumour Exome (ADTEx) is a tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples.

Description

ADTEx estimates copy number alterations and genotypes in whole exome capture of tumour/matched normal samples. Main mathematical models used in ADTEx are discrete wavelet transformation and Hidden Markov Models. It predicts copy number changes in each targeted region and genotypes of SNPs.





Links


References

  1. Amarasinghe KC, Li J, Hunter SM, Ryland GL, Cowin PA, Campbell IG, Halgamuge SK. 2014. BMC Genomics


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