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vtools specifications


Unique identifier OMICS_14512
Name vtools
Alternative name variant tools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format VCF
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.7.0
Stability Stable
Maintained Yes




No version available



  • person_outline Bo Peng

Additional information


Publication for variant tools

vtools citations


Genome wide association analysis identifies new candidate risk loci for familial intracranial aneurysm in the French Canadian population

Sci Rep
PMCID: 5847615
PMID: 29531279
DOI: 10.1038/s41598-018-21603-7

[…] ci from the GWAS signals that have reached suggestive level of association in the exome sequencing results of 32 selected FC IA cases and 106 FC controls. Variable Thresholds Test (VT) implemented in Variant Tools (Vtools) and Sequence Kernel Association Test (SKAT) were performed to test the exonic variation burden in the genes located in the GWAS significant regions.Thirty-four Nunavik Inuit (Qu […]


Strategies for identification of somatic variants using the Ion Torrent deep targeted sequencing platform

BMC Bioinformatics
PMCID: 5753459
PMID: 29301485
DOI: 10.1186/s12859-017-1991-3

[…] ller (TVC) [] and then constructed a straightforward tumor-normal variant subtraction routine by comparing the VCFs produced by TVC, a method we dubbed the “Poor Man’s somatic detector” (PM). We used Variant Tools [] to annotate the variants for each method with data from ANNOVAR [], the 1000 Genomes Project (1 KG) [] and the Exome Variant Server (EVS) []. For each method, we then excluded variant […]


Diagnostic outcomes of exome sequencing in patients with syndromic or non syndromic hearing loss

PLoS One
PMCID: 5749682
PMID: 29293505
DOI: 10.1371/journal.pone.0188578
call_split See protocol

[…] Variants were stored and annotated in the variant collection and annotation system, based on vtools and ANNOVAR software. Refseq gene models were used for transcript positioning of variants and annotations from dbSNP v138 were used for single nucleotide polymorphism (SNP) annotation. The Slov […]


Identification of potential genetic causal variants for rheumatoid arthritis by whole exome sequencing

PMCID: 5762310
PMID: 29340042
DOI: 10.18632/oncotarget.22630

[…] with GATK v3.7 (https://software.broadinstitute.org/gatk/). Default settings were used for BWA, SAMtools, Picard and GATK tools.Further filtration for the joint genotyped variants was performed using Variant Tools []. We applied the following filters to generate a list of preliminary variants by removing false-positive variants through Variant Quality Score Recalibration with tranche truth sensiti […]


Mutational profile of rare variants in inflammasome related genes in Behçet disease: A Next Generation Sequencing approach

Sci Rep
PMCID: 5559572
PMID: 28814775
DOI: 10.1038/s41598-017-09164-7

[…] The association of the rare variants of each gene with the diseases was evaluated for using Variant Tools software, . For patient data, the 71 calling files from Ion Reporter were randomly splitted in 5 files with GATK (Broad Institute, MA) to conserve number of samples (n = 355), these VCF […]


Rare genetic variation in UNC13A may modify survival in amyotrophic lateral sclerosis

PMCID: 5125285
PMID: 27584932
DOI: 10.1080/21678421.2016.1213852
call_split See protocol

[…] genes was extracted, including introns and 500bp upstream and downstream. A gene-based SKAT test () was conducted to compare burden of rare variation in the two groups. SKAT analysis was conducted in Variant Tools () and Variant Association Tools () by implementation of the R package ‘SKAT’ (http://cran.r-project.org/web/packages/SKAT/). This implementation of SKAT generates empirical p-values and […]


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vtools institution(s)
Department of Epidemiology, University of Texas, MD Anderson Cancer Center, TX, USA; Program in Biomathematics and Biostatistics, University of Texas Graduate School of Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Genetics, University of Texas, MD Anderson Cancer Center, TX, USA
vtools funding source(s)
Supported by National Institutes of Health (grants R01AR044422, U01 GM 92666, 5R03CA143982 and 1R01HG005859); Schissler Foundation; Lyda Hill Foundation.

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