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CONTRA specifications

Information


Unique identifier OMICS_00331
Name CONTRA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages Python, R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Publication for CONTRA

CONTRA in pipelines

 (2)
2017
PMCID: 5574920
PMID: 28851938
DOI: 10.1038/s41598-017-09247-5

[…] by gatk printreads was used for variant calling. for the above described analyses, we used algorithms imbedded in gatk software tools (version 3.3.0; http://www.broadinstitute.org). cnvnator and contra were used to detect copy number variations., before discovering single nucleotide variants (snvs), indels, and copy number variants (cnvs), we analyzed coverage in the targeted exons […]

2015
PMCID: 4872731
PMID: 25987131
DOI: 10.18632/oncotarget.3731

[…] allele fraction between matched tumor and normal samples. the sift algorithm was used to predict the putative effect of each nonsynonymous mutation on protein function []. control-freec [] and contra [] were used to infer copy number changes from wgs and wes data, respectively, and the following criteria were applied for gene-level copy number estimation: 1) segments with log2-ratio > […]


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CONTRA in publications

 (27)
PMCID: 5701046
PMID: 29170503
DOI: 10.1038/s41467-017-01460-0

[…] mutation data can be found as supplementary data . statistical analyses of total mutational load are based on all mutations found in a particular sample. dna copy number data were generated using contra version 2.0.3, and data were segmented using glad. dna copy number data derived from wes data can be found as supplementary data . subclonality of mutations in the form of ‘cancer cell […]

PMCID: 5668369
PMID: 29097733
DOI: 10.1038/s41598-017-14962-0

[…] mutect and somatk-snv (developed by bgi, manuscript in preparation), and indels were detected using gatk and somatk-indel (developed by bgi, manuscript in preparation). cnv calling was applied by contra (v2.0.4). the cnv analysis was performed based on off-target sequencing data, which is used as low-depth whole genome sequencing data described in research by bellos e et al.. we split […]

PMCID: 5739621
PMID: 29285234
DOI: 10.18632/oncotarget.21349

[…] preparation). a minimal amplicon coverage of 300 was defined, and a variant allele frequency of 1% as theminimal threshold was used to provide reliable diagnostic analysis. cnv calling was done by contra v2.0.4 []. we defined a gene as showing copy number gain when its coverage fold ratio was ≥2.0 and loss when ≤0.5., the experimental data are presented as the mean±sem and were analyzed […]

PMCID: 5574920
PMID: 28851938
DOI: 10.1038/s41598-017-09247-5

[…] by gatk printreads was used for variant calling. for the above described analyses, we used algorithms imbedded in gatk software tools (version 3.3.0; http://www.broadinstitute.org). cnvnator and contra were used to detect copy number variations., before discovering single nucleotide variants (snvs), indels, and copy number variants (cnvs), we analyzed coverage in the targeted exons […]

PMCID: 5452530
PMID: 28569140
DOI: 10.1186/s12859-017-1705-x

[…] of (1) ability to detect somatic aberration, (2) using read depth (rd) method and (3) was published in the recent years or commonly used. six tools meet the above criteria: (1) adtex [], (2) contra [], (3) cn.mops [], (4) exomecnv [], (5) varscan2 [], and (6) convex []. adtex and convex were developed by the same group using a similar method, which adtex is the modified version […]


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CONTRA institution(s)
Bioinformatics Core Facility, Peter MacCallum Cancer Centre, VIC, Australia

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