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ADTEx specifications


Unique identifier OMICS_03365
Name ADTEx
Alternative names Aberration Detection in Tumour Exome, CoNVEX
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python, R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


Publication for Aberration Detection in Tumour Exome

ADTEx citations


SMAD4 and NF1 mutations as potential biomarkers for poor prognosis to cetuximab based therapy in Chinese metastatic colorectal cancer patients

BMC Cancer
PMCID: 5921972
PMID: 29703253
DOI: 10.1186/s12885-018-4298-5
call_split See protocol

[…] SNPs. Mutations identified within the whole blood controls were subtracted to exclude germline mutations where applicable. Structural variants were detected using FACTERA with default parameters []. ADTEx ( was used to identify copy number variations (CNVs) with default parameters. All the genetic alterations identified were manually reviewed on Integrative Genomics […]


Targeted next generation sequencing identified clinically actionable mutations in patients with esophageal sarcomatoid carcinoma

BMC Cancer
PMCID: 5838991
PMID: 29506494
DOI: 10.1186/s12885-018-4159-2

[…] inimum base quality = 15, minimum variant allele frequency (VAF) = 0.01, minimum variant supporting reads = 5, variant supporting reads mapped to both strands, and strand bias no greater than 10% []. ADTEx ( was used to identify copy number variations (CNVs) using a normal human HapMap DNA sample NA18535, and the cutoff of log2 ratio was set at ±0.6 for copy number cha […]


Integrated Molecular Characterization of Gastrointestinal Stromal Tumors (GIST) Harboring the Rare D842V Mutation in PDGFRA Gene

Int J Mol Sci
PMCID: 5877593
PMID: 29510530
DOI: 10.3390/ijms19030732

[…] f on protein function and stability.Moreover, on paired tumor/normal WES data, the analysis of amplifications and large deletions was performed applying two different tools, Control FREEC v7.2 [] and ADTEX v2.0 []. A consensus method was implemented with the aim of selecting the overlapping regions given by the two algorithms (overlap of gain or loss ≥ 80%) followed by a downstream filtering proce […]


NSAID use and somatic exomic mutations in Barrett’s esophagus

Genome Med
PMCID: 5830331
PMID: 29486792
DOI: 10.1186/s13073-018-0520-y

[…] t NSAID use slowed or reduced the accumulation of somatic chromosomal alterations (SCA) []. In our study, SCA was quantified from exome data using an expanded algorithm based on a modified version of ADTEx (Additional file : Table S15) and binned into SCA classes including homozygous deletions (HD), copy loss, cnLOH, balanced gain (> 2 N copies with balanced allele-specific copy number), allele-sp […]


Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis enriched mutations in the A kinase anchoring protein family (AKAPs)

BMC Cancer
PMCID: 5810006
PMID: 29433456
DOI: 10.1186/s12885-018-4021-6

[…] around known indels and base-quality recalibrated by GATK. Somatic single nucleotide variants (SNVs) were detected by Mutect [] with the high-confidence mode. Copy number alterations were detected by ADTEx []. All pipelines and analyses were run using Anduril [], a workflow framework for scientific data analysis. Mean coverage per sample is given in (Additional file : Figure S2b). […]


Single cell profiling of human gliomas reveals macrophage ontogeny as a basis for regional differences in macrophage activation in the tumor microenvironment

Genome Biol
PMCID: 5738907
PMID: 29262845
DOI: 10.1186/s13059-017-1362-4
call_split See protocol

[…] /) and the GATK toolkit [] carried out quality score re-calibration, duplicate-removal, and re-alignment around indels. Large-scale (>100 Exons) somatic copy number variants (CNVs) were inferred with ADTex []. To increase CNV size, proximal (< 1 Mbp) CNVs were merged. Somatic SNVs were inferred with MuTect ( for each tumor/control pair and annotated […]


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ADTEx institution(s)
Department of Mechanical Engineering, University of Melbourne, Parkville, VIC, Australia

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