VIVA (VIsualization of VAriants): A VCF File Visualization Tool

Tollefson, George A.; Schuster, Jessica; Gelin, Fernando; Agudelo, Anthony; Ragavendran, Ashok; Restrepo, Iván; Stey, Paul; Padbury, Jamés F.; Uzun, Alper

doi:10.1038/s41598-019-49114-z

Cited by 14 publications

(15 citation statements)

References 10 publications

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“…We have compared the main features of re-Searcher with other existing and open source tools VIVA ( Tollefson et al, 2019 ), VCFtools ( Danecek et al, 2011 ), GEMINI ( Paila et al, 2013 ), BrowseVCF ( Salatino & Ramraj, 2016 ), VCF.Filter ( Müller et al, 2017 ), VCF-Miner ( Hart et al, 2016 ) and prepared a detailed table ( Table 1 ). The compared tools have been developed and implemented in different programming languages (Julia, C++, Perl, Java and Python) and dedicated libraries.…”

Section: Resultsmentioning

confidence: 99%

re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files

Karabayev

Molkenov

Yerulanuly

et al. 2021

PeerJ

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Background High-throughput sequencing platforms generate a massive amount of high-dimensional genomic datasets that are available for analysis. Modern and user-friendly bioinformatics tools for analysis and interpretation of genomics data becomes essential during the analysis of sequencing data. Different standard data types and file formats have been developed to store and analyze sequence and genomics data. Variant Call Format (VCF) is the most widespread genomics file type and standard format containing genomic information and variants of sequenced samples. Results Existing tools for processing VCF files don’t usually have an intuitive graphical interface, but instead have just a command-line interface that may be challenging to use for the broader biomedical community interested in genomics data analysis. re-Searcher solves this problem by pre-processing VCF files by chunks to not load RAM of computer. The tool can be used as standalone user-friendly multiplatform GUI application as well as web application (https://nla-lbsb.nu.edu.kz). The software including source code as well as tested VCF files and additional information are publicly available on the GitHub repository (https://github.com/LabBandSB/re-Searcher).

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Section: Resultsmentioning

confidence: 99%

re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files

Karabayev

Molkenov

Yerulanuly

et al. 2021

PeerJ

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“…VCFtools is also devoid of visualization functions. Other tools such as MuSiC ( 2 ) and VIVA ( 5 ) can be used for visualization and may also handle some analyses. Nevertheless, these tools provide limited capability that must be complemented by other tools, seriously impeding the efficiency and accuracy of studies in cancer genomics (Table 1 ).…”

Section: Discussionmentioning

confidence: 99%

“…Even though several tools and software packages for probing genomic data have already been developed, distinct formats of input files still make analysis cumbersome. Tools such as Maftools ( 4 ) offer various analyses in a single R package, while VIVA ( 5 ) supports data processing. However, they require still other tools to complement their inability to filter out false-positive mutations and perform data transformation.…”

Section: Introductionmentioning

confidence: 99%

MutScape: an analytical toolkit for probing the mutational landscape in cancer genomics

Tsai

et al. 2021

NAR Genomics and Bioinformatics

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Cancer genomics has been evolving rapidly, fueled by the emergence of numerous studies and public databases through next-generation sequencing technologies. However, the downstream programs used to preprocess and analyze data on somatic mutations are scattered in different tools, most of which require specific input formats. Here, we developed a user-friendly Python toolkit, MutScape, which provides a comprehensive pipeline of filtering, combination, transformation, analysis and visualization for researchers, to easily explore the cohort-based mutational characterization for studying cancer genomics when obtaining somatic mutation data. MutScape not only can preprocess millions of mutation records in a few minutes, but also offers various analyses simultaneously, including driver gene detection, mutational signature, large-scale alteration identification and actionable biomarker annotation. Furthermore, MutScape supports somatic variant data in both variant call format and mutation annotation format, and leverages caller combination strategies to quickly eliminate false positives. With only two simple commands, robust results and publication-quality images are generated automatically. Herein, we demonstrate the ability of MutScape to correctly reproduce known results using breast cancer samples from The Cancer Genome Atlas. More significantly, discovery of novel results in cancer genomic studies is enabled through the advanced features in MutScape. MutScape is freely available on GitHub, at https://github.com/anitalu724/MutScape.

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“…The resulting SNP markers (1,064 in total) were used to visualize the genotypes of the males and queens at LG14 using VIVA (v. 0.4.0) (Tollefson et al 2019). To further characterize the two alleles of the supergene, we performed a PCA on 65 SNP markers identified in the non-recombining area of LG14 (i.e.…”

Section: Methodsmentioning

confidence: 99%

Evolutionary genomics of socially polymorphic populations ofPogonomyrmex californicus

Errbii

Lajmi

et al. 2021

Preprint

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The societies of social insects are highly variable, including variation in the number of reproductives in a colony. In the California harvester ant, Pogonomyrmex californicus (Buckley 1867), colonies are commonly founded by a single queen (haplometrosis, primary monogyny). However, in some populations in California (USA), two or more queens cooperate in colony founding (pleometrosis) and continue to share a nest over several years (primary polygyny). Here, we use population genomics and linkage mapping to study the evolutionary dynamics and genetic architecture of this social niche polymorphism. Our analyses show that both populations underwent consecutive bottlenecks over the last 100,000 generations, particularly decreasing population size in the P-population and that the two populations diverged until 1,000 generations ago, after which gene flow increased again and we found signs of recent genetic admixture between the two populations. We further uncover an 8 Mb non-recombining region segregating with the observed social niche polymorphism, showing characteristics of a supergene comparable to the ones underlying social niche polymorphism in other ant species. In addition, 57 genes in five genomic regions outside the supergene show signatures of a selective sweep in the P-population, some of which are differentially expressed between haplo- and pleometrotic queens during colony founding. Our findings expose the social niche polymorphism in P. californicus as a polygenic trait involving a supergene.

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VIVA (VIsualization of VAriants): A VCF File Visualization Tool

Cited by 14 publications

References 10 publications

re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files

re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files

MutScape: an analytical toolkit for probing the mutational landscape in cancer genomics

Evolutionary genomics of socially polymorphic populations ofPogonomyrmex californicus

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