exomeCopy statistics

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Citations per year

Number of citations per year for the bioinformatics software tool exomeCopy
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Tool usage distribution map

This map represents all the scientific publications referring to exomeCopy per scientific context
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Associated diseases

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Popular tool citations

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Protocols

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

 (8)
library_books

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

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

[…] Prediction 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 […]

call_split

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

2017
Leukemia
PMCID: 5508072
PMID: 27899802
DOI: 10.1038/leu.2016.365
call_split See protocol

[…] 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. […]

library_books

Altools: a user friendly NGS data analyser

2016
Biol Direct
PMCID: 4756442
PMID: 26883204
DOI: 10.1186/s13062-016-0110-0

[…] Scalpel. CNVs are identified with their own in-house developed algorithm. Again, its performance should be compared with other tools for similar purposes (e.g. XHMM, ExomeDepth, Conifer, CONTRA, and exomeCopy). Without such comparison, it is difficult to judge whether Altools’ result are superior to those tools and nobody would use the tool. 2. The pipeline is tightly designed with very limited f […]

call_split

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
call_split See protocol

[…] on1.0; 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. In parallel, […]

call_split

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

2015
Mol Psychiatry
PMCID: 5414091
PMID: 25644381
DOI: 10.1038/mp.2014.193
call_split See protocol

[…] 2 -maxG 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 wind […]

library_books

Identification of copy number variants from exome sequence data

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

[…] CNV, and CNVs containing 1–4 exons were identified. The TP/FP ratio for each program was then calculated (Table ). CoNIFER, ExomeDepth and XHMM did not identify any TP short CNVs. The intersection of ExomeCopy and ExCopyDepth showed the highest TP/FP ratio, demonstrating the ability of ExomeCopy and ExCopyDepth to detect CNVs that cover 1–4 exons with the highest FP CNV count. […]


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

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