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exomeCopy specifications

Information


Unique identifier OMICS_02062
Name exomeCopy
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.26.0
Stability Stable
Requirements
methods, Rsamtools, GenomeInfoDb, Biostrings, stats4, IRanges(>=2.5.27), GenomicRanges(>=1.23.16)
Maintained Yes

Versioning


No version available

Documentation


Publication for exomeCopy

exomeCopy citations

 (7)
library_books

Use of next generation sequencing to detect LDLR gene copy number variation in familial hypercholesterolemia[S]

2017
PMCID: 5665663
PMID: 28874442
DOI: 10.1194/jlr.D079301

[…] of cnvs from ngs data has been investigated previously; however, it remains a relatively new and challenging field. commonly used cnv prediction programs include conifer (), exomedepth (), exomecopy (), xhmm (), and cnv-seq (); however, many of these designated methods have shown high rates of false-positive cnvs, which poses a major limitation on potential clinical use. moreover, many […]

library_books

Genomic and transcriptional landscape of P2RY8 CRLF2 positive childhood acute lymphoblastic leukemia

2017
PMCID: 5508072
PMID: 27899802
DOI: 10.1038/leu.2016.365

[…] ., reads were aligned with bwa-mem and mutations called with mutect. snpeff, dbnsfp and custom perl scripts were used for variant annotation and filtering. wes-based cna detection was performed with exomecopy., total rna was extracted from frozen primary leukemic samples (>90% blasts) upon ficoll gradient separation using quick-rna miniprep kit (zymo research, irvine, ca, usa). selection […]

library_books

Novel Missense Mutation A789V in IQSEC2 Underlies X Linked Intellectual Disability in the MRX78 Family

2016
PMCID: 4707274
PMID: 26793055
DOI: 10.3389/fnmol.2015.00085

[…] emde et al., ) in order to detect short insertions (<30 bp) and larger deletions (<50 kb) from unmapped and indel-containing reads. in addition, large insertions/deletions were predicted using exomecopy (love et al., ) by analysing changes in depth of coverage along the targeted regions. single-nucleotide polymorphisms (snps) and short indels (<5 bp) were called with snpstore. […]

library_books

X exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes

2015
PMCID: 5414091
PMID: 25644381
DOI: 10.1038/mp.2014.193

[…] 50000) to detect short insertions (⩽30 bp) and larger deletions (<50 kb). for detecting large insertions/deletions by analyzing changes in depth of coverage along the targeted regions we used exomecopy. we performed a quality-based clipping of reads after mapping but before calling variants to minimize the number of false-positive calls. starting from each end of a read with a sliding […]

library_books

Identification of copy number variants from exome sequence data

2014
PMCID: 4132917
PMID: 25102989
DOI: 10.1186/1471-2164-15-661

[…] (including shorter cnvs that cover 1–4 exons), combining computational prediction algorithms and a high-resolution custom cgh array., we used six published cnv prediction programs (exomecnv, contra, exomecopy, exomedepth, conifer, xhmm) and an in-house modification to exomecopy and exomedepth (excopydepth) for computational cnv prediction on 30 exomes from the 1000 genomes project and 9 exomes […]

library_books

Comparative Study of Exome Copy Number Variation Estimation Tools Using Array Comparative Genomic Hybridization as Control

2013
PMCID: 3835197
PMID: 24303503
DOI: 10.1155/2013/915636

[…] the last few years, but the performance and accuracy of these programs have not been thoroughly evaluated. in this study, we systematically compared four popular exome cnv tools (conifer, cn.mops, exomecopy, and exomedepth) and evaluated their effectiveness against array comparative genome hybridization (array cgh) platforms. we found that exome cnv tools are capable of identifying cnvs, […]


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exomeCopy institution(s)
Max Planck Institute for Molecular Genetics, Berlin, Germany

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