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Protocols

EXCAVATOR specifications

Information


Unique identifier OMICS_00332
Name EXCAVATOR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Romi D'Aurizio

Publications for EXCAVATOR

EXCAVATOR citations

 (27)
library_books

An integrated clinical and genomic information system for cancer precision medicine

2018
BMC Med Genomics
PMCID: 5918454
PMID: 29697362
DOI: 10.1186/s12920-018-0347-9

[…] equencing (WTS, a.k.a. RNA-seq) data. We calculate the somatic single nucleotide variants (SNVs), insertions and deletions (INDELs), and copy number variations (CNVs) using Mutect [], Strelka [], and EXCAVATOR [], respectively. The MapSplice-RSEM [, ] pipeline was used for RNA-seq quantification to warrant accuracy in spite of long computation time. Galaxy [] pipelines for WES and WTS data process […]

library_books

Xome Blender: A novel cancer genome simulator

2018
PLoS One
PMCID: 5886411
PMID: 29621252
DOI: 10.1371/journal.pone.0194472

[…] number and identify significant change-points and finally, merges adjacent segments of similar copy number and classify them as either large-scale (>25% of chromosome arm) or focal events (<25%) []. EXCAVATOR2 is based on the RC approach, unlike its previous version (EXCAVATOR), it enhances the identification of genomic CNVs (overlapping or non-overlapping exons) from WES data by integrating the […]

library_books

Characterization of brain tumor initiating cells isolated from an animal model of CNS primitive neuroectodermal tumors

2018
Oncotarget
PMCID: 5862611
PMID: 29568390
DOI: 10.18632/oncotarget.24460

[…] TK tools [], which includes duplicated reads removing, local realignment around indels, base quality recalibration. All these procedures were performed prior to mutation detection. We made use of the EXCAVATOR algorithm [] to do the CNV detection. EXCAVATOR was run with the default settings. SG-ADVISER [] was applied to derive functional effects from predicted CNVs. […]

library_books

Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution

2018
Nat Commun
PMCID: 5750210
PMID: 29296022
DOI: 10.1038/s41467-017-02424-0

[…] to correct the mutation VAFs or copy number estimates in the rest of the analyses.The CCF of each mutation was calculated by integrating the above mentioned purity estimates and the copy numbers from EXCAVATOR, using the approach of McGranahan et al. In brief, the VAF of each mutations, given the CCF, can be calculated as follows:VAFCCF=p*CCF∕CNn*1-p+p*CNtwhere p is the tumor purity, and CNt and C […]

library_books

Exome and transcriptome sequencing identifies loss of PDLIM2 in metastatic colorectal cancers

2017
PMCID: 5685135
PMID: 29184442
DOI: 10.2147/CMAR.S149002

[…] . Point mutations were identified using the MuTect tool (https://github.com/broadinstitute/mutect) with paired samples. Perl script and Annovar were used to annotate variants. CNVs were identified by EXCAVATOR. Significant focal somatic copy number alterations were summarized by GISTIC analysis. […]

call_split

The genomic landscape of malignant peripheral nerve sheath tumors: diverse drivers of Ras pathway activation

2017
Sci Rep
PMCID: 5678116
PMID: 29118384
DOI: 10.1038/s41598-017-15183-1
call_split See protocol

[…] athway, we utilized the DAVID tool (https://david.ncifcrf.gov/) for pathway mapping.Copy number analysis from in-house whole exome sequencing data was performed via paired tumor-normal analysis using EXCAVATOR. Results were further filtered to include only segments with ProbCall >0.9 for novel findings or >0.5 for previously described recurrent CNV in this disease. To further focus on likely patho […]

Citations

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EXCAVATOR institution(s)
Laboratory of Integrative Systems Medicine (LISM), Institute of Informatics and Telematics and Institute of Clinical Physiology, National Research Council, Pisa, Italy; Medical Genetics Unit, Sant'Orsola Malpighi Polyclinic, Bologna, Italy; Department of Computer Science, University of Pisa, Pisa, Italy; Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
EXCAVATOR funding source(s)
Flagship project InterOmics (PB. P05, CUP B91J12000270001), Italian Ministry for Instruction University and Research (MIUR) and CNR organisations; Italian Ministry of Health, Young Investigators Award for the Project GR-2011-02352026 ‘Detecting copy number variants from whole-exome sequencing data applied to acute myeloid leukemias’

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