CNVnator protocols

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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Documentation


Maintainers


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

Publication for CNVnator

CNVnator IN pipelines

 (12)
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 [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 […]

2017
PMCID: 5693876
PMID: 29180989
DOI: 10.3389/fmicb.2017.02210

[…] the average sequencing depth was around 110x. to detect genetic alterations, clean reads obtained from genome sequencing were mapped to the reference genome of gt1, and samtools, breakdancer and cnvnator were used to detect short indels, structural variations (insertion, deletion, and inversion) and copy number variations, respectively (chen et al., 2009; li et al., 2009; abyzov et al., […]

2017
PMCID: 5701311
PMID: 28696212
DOI: 10.1101/mcs.a001909

[…] 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 […]

2017
PMCID: 5701311
PMID: 28696212
DOI: 10.1101/mcs.a001909

[…] and 1000 genomes projects (the 1000 genomes project consortium 2015). bioinformatic identification of cnvs was performed using default parameters of breakdancer (v 1.4.5) (chen et al. 2009) and cnvnator (v 0.3) (abyzov et al. 2011)., wgs alignments and regional variation in read coverage were viewed using the integrated genomics viewer (igv, 2.3.55) […]

2016
PMCID: 5066660
PMID: 26821983
DOI: 10.1111/pbi.12528

[…] 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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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)
.........