EXCAVATOR protocols

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EXCAVATOR statistics

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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

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Documentation


Maintainer


  • person_outline Romi D'Aurizio <>

Publications for EXCAVATOR

EXCAVATOR in pipeline

2016
PMCID: 5349924
PMID: 27835906
DOI: 10.18632/oncotarget.13239

[…] mutations were checked if they were transcribed or edited in rna. a full list of mutations is presented in ., somatic copy number alterations (cnas) were identified in eight tumor–normal pairs using excavator [] in somatic mode. for two unpaired samples (s5 and f5), we used excavator in pooling mode to compare each tumor sample with a mean of the eight normal (ns1–4 and nf1–4) samples. excavator […]


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EXCAVATOR in publications

 (19)
PMCID: 5918454
PMID: 29697362
DOI: 10.1186/s12920-018-0347-9

[…] (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 […]

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

[…] 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., total rna isolation […]

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

[…] reads were considered. the somatic mutations were annotated using the ensembl variant effect predictor tool. somatic copy number estimations were derived from the exome-sequencing data using excavator by calculating log2 ratios between the read depth of the tumor and two germline skin samples using the “pool” mode. the estimated log2 ratios were then segmented by their novel […]

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., the reads from the fastq files were mapped against the hg19 human reference genome using tophat […]

PMCID: 5627939
PMID: 28977029
DOI: 10.1371/journal.pone.0185826

[…] ≥ 20× and alternative allele frequency of ≥ 20% in tumor and 0% in blood. the variants were annotated by annovar (http://www.openbioinformatics.org/annovar/). copy number variants were detected by excavator, a package developed for interpreting whole-exome sequencing data []., whole-transcriptome sequencing (wts) was performed on the sample collected in 2013. the captured mrna was sequenced […]


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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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