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PopSV specifications


Unique identifier OMICS_17837
Name PopSV
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes




No version available



  • person_outline Guillaume Bourque

Publication for PopSV

PopSV citations


5 Hydroxymethylcytosine signatures in cell free DNA provide information about tumor types and stages

Cell Res
PMCID: 5630676
PMID: 28820176
DOI: 10.1038/cr.2017.106

[…] track of hg19 from ucsc (kmer = 75). bins with mappability score under 0.8 were eliminated from further analysis. gc content percentages in each bin were calculated using getgc.hg19 from r package popsv (1.0.0) and gc bias was corrected by fitting a loess model (correct.gc from r package popsv 1.0.0). the corrected bin counts were then scaled by mean bin count of each sample and centered at 2. […]


Loss of chromosome Y leads to down regulation of KDM5D and KDM6C epigenetic modifiers in clear cell renal cell carcinoma

Sci Rep
PMCID: 5362952
PMID: 28332632
DOI: 10.1038/srep44876

[…] of cells with loy was (0.5-coverage)/0.5., we used a logistic regression to test the association of loy with age. finally, the cnvs used for kdm5c or kdm6a deletion investigation were detected by popsv using the normal samples as reference and 5 kbp bins., to examine the status of loy in dna of tumor and blood samples, y chromosome deletion detection system assay, version 2 (promega, wi, usa) […]

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PopSV institution(s)
Department of Human Genetics, McGill University, Montreal, QC, Canada; McGill University and Genome Quebec Innovation Center, Montreal, QC, Canada; Centre de Recherche du Centre Hospitalier de l’Universite de Montreal, Montreal, QC, Canada; Montreal Neurological Institute, McGill University, Montreal, QC, Canada; Departement des sciences fondamentales, Universite du Quebec a Chicoutimi, Chicoutimi, QC, Canada
PopSV funding source(s)
Supported by a grant from the National Sciences and Engineering Research Council (NSERC-448167-2013), a grant from the Canadian Institute for Health Research (CIHR-MOP-115090), the Fonds de Recherche Sante Quebec (FRSQ-29493 and FRSQ-25348) and the Netherlands Organization for Scientific Research under award number 184021007, and made available as a Rainbow Project of the Biobanking and Biomolecular Research Infrastructure Netherlands (BBMRI-NL).

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