CNVnator pipeline

CNVnator specifications


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

Publication for CNVnator

CNVnator citations

PMCID: 5701311

[…] bordered by discordant reads encompassing exon 1 encoding the 5′ untranslated region (5′ utr) (fig. 3). the candidate deletion was also detected by copy-number variant detection algorithms: cnvnator (based on alterations in read depth) and breakdancer (based on paired-end information) (chen et al. 2009; abyzov et al. 2011). the precise breakpoints were mapped by pcr and sanger […]

PMCID: 5513543

[…] (janoušek et al. 2013) on the abp gene region by identifying and comparing cnvs in the abp gene family of wild m.musculus samples. using the c57bl/6 genome (2011, mm10) as a reference, we plotted cnvnator-predicted cnv calls in the abp region as a heat map which helps to visualize differences in cn. we compared the calls from 27 wild mmd mice (fig. 1) from four different localities: […]

PMCID: 5371188

[…] retrieved from the ucsc website ( to save run time during the downstream analysis, we converted the sam files to bam files and then sorted and merged them by samtools [74]., cnvnator was run on merged bam files with a bin size of 200 bp following the authors’ recommendations [65]. after calling, quality control was performed on the raw cnvs for each bull. the filtering […]

PMCID: 5066660

[…] variants (snps and indels) were reported only if the variant call was present in a particular accession and reference allele was present in remaining accessions. for identification of cnvs, cnvnator tool was used with an e‐value of 1e‐05 (abyzov et al., 2011). raw reads from asha (icpl 87119) genotype were aligned to draft assembly (asha) for detecting the false positives in cnvs. […]

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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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:
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)