CNV-seq protocols

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description
CNV-seq computational protocol

CNV-seq specifications

Information


Unique identifier OMICS_00339
Name CNV-seq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Aligned read positions
Operating system Unix/Linux, Mac OS
Programming languages Perl, R
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for CNV-seq

CNV-seq IN pipelines

 (4)
2016
PMCID: 5072345
PMID: 27760518
DOI: 10.1186/s12711-016-0257-2

[…] file that included all three aa bulls and one bam file that included all five gg bulls using samtools [16], which were used to identify larger segregating structural variations in the genome by the cnv-seq software [23]. significant results were initially examined and visually inspected using the integrative genomics viewer software (igv [24]), and confirmed by pcr on a larger number […]

2013
PMCID: 3730349
PMID: 23814129
DOI: 10.1093/gbe/evt097

[…] the minimum alignment length of read (min_num_matched_bases) = 30, the minimum mapping quality of the reads pindel uses as anchor (anchor_quality) = 20., putative cnvs were identified using the cnv-seq, which examines the mapped reads from two individual chickens and reports regions that exhibit significant read depth differences (xie and tammi 2009). the following parameters were used […]

2013
PMCID: 3787092
PMID: 24098698
DOI: 10.1371/journal.pone.0075485

[…] (canfam 2, may 2005) using the bioscope (lifetechnologies) software pipeline. duplicate and low quality reads were removed using the picard tools (http://picard.sourceforge.net)., the program cnv-seq was used to calculate ratios (expressed as log2) and p-values for each tumor/pbmc pair using globally normalized read densities in sliding windows [41]. the confidence level used to calculate […]

2011
PMCID: 3308051
PMID: 21917144
DOI: 10.1186/gb-2011-12-9-r88

[…] in td relative to ld in a sliding window. the observed ratios were statistically assessed by estimating the probability of a random occurrence, given no cnv, using the method implemented in the cnv-seq software [69]. only those targets that had at least four overlapping 500-bp windows (250-bp overlap) showing a statistically significant log2 coverage ratio were classified as cnvs. […]

CNV-seq institution(s)
Department of Biological Sciences, National University of Singapore, Singapore; Department of Biochemistry, National University of Singapore, Singapore; Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
CNV-seq funding source(s)
Supported by National University of Singapore FRC grant number R154000265112 and a National University of Singapore Research Scholarship.

CNV-seq review

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Antoine Rousselin

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Desktop
I have been using this tool since 2009 for the detection of CNV in genes predisposed to breast and ovarian cancer. After having modified a little original script, adapt the parameters this software is very precise (specificity, sensitivity). But it is not suitable for analysis on a large panel of genes.