ExomeCNV protocols

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ExomeCNV statistics

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ExomeCNV specifications

Information


Unique identifier OMICS_00333
Name ExomeCNV
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.4
Stability Stable
Maintained Yes

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Publication for ExomeCNV

ExomeCNV in pipelines

 (5)
2017
PMCID: 5290635
PMID: 28153049
DOI: 10.1186/s13073-017-0401-9

[…] iously in []. we calculated the clonality rate of mutations based on the variant allele frequency, ploidy at the site, and the admixture rate []. we performed the cnv analysis on all tumors using the exomecnv package []. we used breakdancer [] to call breakpoints, applied filtering on the raw calls, and performed annotation using annovar (additional file )., we used the mclust package in r (http:/ […]

2016
PMCID: 4762880
PMID: 26891683
DOI: 10.1038/ncomms10690

[…] tool, bwa aln. somatic single-nucleotide variants (compared with pc9-1) were called using mutect with default parameters. somatic copy number variations (cnvs; compared with pc9-1) were called using exomecnv with default parameters to provide a specificity and sensitivity of 99.99%. cnvs with read ratios in the range 0.6<ratio<1.4 were filtered out., variants called reflect a difference […]

2015
PMCID: 4597064
PMID: 26424171
DOI: 10.1186/1471-2105-16-S13-S7

[…] sort, and reorder aligned reads (picard tools v1.119 []). gatk v3.3-0 [] was used to perform local realignment and base quality recalibration. copy number data was computational inferred using exomecnv v1.4 []. single nucleotide variants (snvs) and small insertions and deletions (indels) were called using strelka v1.0.14 [] (tumor and normal pairs), resulting in variant call format (vcf) […]

2014
PMCID: 4162913
PMID: 25167919
DOI: 10.1186/1471-2164-15-732

[…] and perform poorly when applied to the detection of somatic cnas in tumour samples. control-freec [] is a method developed for wgs tumour data and more recently supports the application to wes data. exomecnv [] and varscan 2 [] are designed for cna identification in tumour wes data, however, they do not predict absolute copy number in non-diploid samples. other methods can predict absolute copy […]

2013
PMCID: 3832364
PMID: 24260384
DOI: 10.1371/journal.pone.0080397

[…] treatment-resistant clone-unique mutations and to find commonly mutated sites, genes, and pathways among the different clones. copy number variation (cnv) and loss of heterozygosity were analyzed by exomecnv., each experiment was set up in duplicate or triplicate, and repeated at least twice. data were expressed as means ± sd and analyzed using one-way anova tests, depending on homogeneity […]


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ExomeCNV in publications

 (42)
PMCID: 5928087
PMID: 29713003
DOI: 10.1038/s41467-018-04129-4

[…] from the online genepattern tools. we used gatk to estimate depth of coverage from the bam files of 186 smc tumor/normal samples using hg19 as genome reference. cnv segmentation was then called by exomecnv v1.4 based on coverage estimates and further annotated to derive copy number value for each gene., we applied three methods for classifying molecular intrinsic subtypes—ihc, pam50, and nmc. […]

PMCID: 5690647
PMID: 29145505
DOI: 10.1371/journal.pone.0188228

[…] below 37. depth of coverage at each position targeted by the nextera exome capture kit was calculated using gatk “depthofcoverage” tool [] and the resulting tumour and normal profiles input to exomecnv r package using default parameters []. gene level log2 copy number ratios were then parsed using custom perl scripts, with those achieving |log2 ratio| > 0.50 taken forward […]

PMCID: 5649057
PMID: 29052513
DOI: 10.1186/s12920-017-0296-8

[…] calls allele specific copy number and assigns both mutations and copy number alterations to clonal sample fractions. there are number of other tools that call allele specific copy number such as exomecnv [] and sequenza [], but these require a tumor/normal pair and do not identify subclones. there are also a number of tools that detect subclonal populations from mutations such as pyclone [], […]

PMCID: 5593152
PMID: 28630369
DOI: 10.1101/mcs.a001859

[…] patient sample and control samples were calculated using gatk-depth of coverage tool. segments with copy-number variations (cnvs) were identified from the log ratio of depth of coverage using the exomecnv r package (). false-positive cnv events were identified and corrected for by calculating minor allele frequencies in each cnv segment., whole-exome sequencing data are not publicly available […]

PMCID: 5455120
PMID: 28577549
DOI: 10.1186/s12885-017-3382-6

[…] for each tumour exome and matching normal sample calculated by gatk. normalized and log transformed read count ratios were then used to identify regions of amplification and deletion with exomecnv []. segmentation was performed using dnacopy [] and segmented data was used as input for the genetic identification of significant targets in cancer version 2.0 (gistic2.0) program [] […]


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