CNVnator protocols

View CNVnator computational protocol

CNVnator statistics

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CNVnator specifications

Information


Unique identifier OMICS_00343
Name CNVnator
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 0.3.3
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Mark Gerstein <>
  • person_outline Alexej Abyzov <>

Publication for CNVnator

CNVnator in pipelines

 (24)
2018
PMCID: 5825990
PMID: 29515596
DOI: 10.3389/fpls.2018.00021

[…] prunus persica (verde et al., ) reference genome assembly v. 2.0 using the bowtie2 short read aligner tool (langmead and salzberg, ). gene cnv was performed with a sliding window of 100 bp and the cnvnator prediction algorithm (abyzov et al., ). cnvnator output was converted to tabular format with in-house scripts and combined with the peach gene annotation files for analysis of genes. coding […]

2018
PMCID: 5883058
PMID: 29615708
DOI: 10.1038/s41598-018-23802-8

[…] individually analyzed visualizing the change-related coordinates of every snapshot produced by igv., bam files resulting from the mapping with super were analyzed in order to get a list of cnvs with cnvnator v0.3.2. bin size was set at 100 bp after several trials in order to have a ratio between average read depth (rd) and standard deviation near 4. several filtering criteria were used […]

2017
PMCID: 5267451
PMID: 28122487
DOI: 10.1186/s12711-017-0286-5

[…] are sensitive to small and medium-sized sv because of the limit set on insert size while snp chip data only capture large sv. one potential better comparison would be to use an rd method such as cnvnator [] and jointslm [] that target large sv events and then to compare them with sv from snp chip data., another consideration is that sv detection from wgs data relies on differences […]

2017
PMCID: 5371188
PMID: 28356085
DOI: 10.1186/s12864-017-3636-3

[…] retrieved from the ucsc website (http://genome.ucsc.edu/). to save run time during the downstream analysis, we converted the sam files to bam files and then sorted and merged them by samtools []., cnvnator was run on merged bam files with a bin size of 200 bp following the authors’ recommendations []. after calling, quality control was performed on the raw cnvs for each bull. the filtering […]

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

[…] file generated 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 […]


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CNVnator in publications

 (91)
PMCID: 5941560
PMID: 29739316
DOI: 10.1186/s12864-018-4718-6

[…] of sequence information to identify specific categories of variants. our variant caller suite consisted of four distinct tools and algorithms: the genome analysis toolkit, pindel, breakdancer, and cnvnator [–]., the genome analysis toolkit (gatk) from the broad institute uses de bruijn graph-based models to identify single-nucleotide substitutions and small insertions and deletions. pindel’s […]

PMCID: 5923231
PMID: 29703896
DOI: 10.1038/s41467-018-03990-7

[…] or evolved (as factor) with impact class (as factor) was significant by comparing a binomial glm with the interaction and without the interaction., in order to identify copy number, we used cnvnator (url: https://github.com/abyzovlab/cnvnator) with 1 kb sliding windows. we identified regions with significant copy number change by comparing copy numbers of each clone in every replicate […]

PMCID: 5884823
PMID: 29644095
DOI: 10.1038/s41525-018-0049-4

[…] mapped to genetic diagnoses., trio blood samples were obtained where possible. rwgs was performed to ~45-fold coverage as previously described., structural variants were identified with manta and cnvnator, a combination that provided the highest sensitivity and precision on 21 samples with known structural variants., structural variants were filtered to retain those affecting coding regions […]

PMCID: 5883058
PMID: 29615708
DOI: 10.1038/s41598-018-23802-8

[…] individually analyzed visualizing the change-related coordinates of every snapshot produced by igv., bam files resulting from the mapping with super were analyzed in order to get a list of cnvs with cnvnator v0.3.2. bin size was set at 100 bp after several trials in order to have a ratio between average read depth (rd) and standard deviation near 4. several filtering criteria were used […]

PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] augustus and annotated by blastp against ncbi non-redundant protein database (e-value ≤1e-5), blast2go and interproscan v.5.22–61.0 against pfam v.30.0. copy-number gains were analyzed with cnvnator v.0.3.3 [] using deduplicated bam files. regions with putative copy number gains were extracted using a bin size of 80 bp recommended by the software and filtered with p-value < 0.05 […]


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CNVnator institution(s)
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Psychiatry and Behavioral Sciences, School of Medicine, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA; Department of Computer Science, Yale University, New Haven, CT, USA
CNVnator funding source(s)
Supported by the NIH and from the AL Williams Professorship funds; by the Yale University Biomedical High-Performance Computing Center, its support team, and NIH grant RR19895.

CNVnator review

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huangli

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Desktop
hi! I have a problerm in using this tool, hope for your help!!!
it's an error in cnvnator -root -partition
the error file is very big and for example like this:
$head WB-l.CNV.call.sh.e7336323
Abnormal range (0, -1)
Abnormal range (1, 0)
Abnormal range (2, 1)
Abnormal range (3, 2)
Abnormal range (4, 3)
Abnormal range (5, 4)
Abnormal range (6, 5)
Abnormal range (7, 6)
Abnormal range (9, 8)
Abnormal range (10, 9)
.........