GenomeVIP: a cloud platform for genomic variant discovery and interpretation.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28522612", "kind": "science-record", "revision": 4, "content_hash": "sha256:d9e7738ba3d5d50fc1783be42da91e704ba9d74b51b6ad3d18192c26e62d1588", "created_at": "2026-11-01T15:40:26Z", "updated_at": "2026-11-01T21:20:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "GenomeVIP: a cloud platform for genomic variant discovery and interpretation.", "doi": "10.1101/gr.211656.116", "pmid": "28522612", "authors": ["R Jay Mashl", "Adam D Scott", "Kuan-Lin Huang", "Matthew A Wyczalkowski", "Christopher J Yoon", "Beifang Niu", "Erin DeNardo", "Venkata D Yellapantula", "Robert E Handsaker", "Ken Chen", "Daniel C Koboldt", "Kai Ye", "David Fenyö", "Benjamin J Raphael", "Michael C Wendl", "Li Ding"], "journal": "Genome research", "year": 2017, "abstract": "Identifying genomic variants is a fundamental first step toward the understanding of the role of inherited and acquired variation in disease. The accelerating growth in the corpus of sequencing data that underpins such analysis is making the data-download bottleneck more evident, placing substantial burdens on the research community to keep pace. As a result, the search for alternative approaches to the traditional \"download and analyze\" paradigm on local computing resources has led to a rapidly growing demand for cloud-computing solutions for genomics analysis. Here, we introduce the Genome Variant Investigation Platform (GenomeVIP), an open-source framework for performing genomics variant discovery and annotation using cloud- or local high-performance computing infrastructure. GenomeVIP orchestrates the analysis of whole-genome and exome sequence data using a set of robust and popular task-specific tools, including VarScan, GATK, Pindel, BreakDancer, Strelka, and Genome STRiP, through a web interface. GenomeVIP has been used for genomic analysis in large-data projects such as the TCGA PanCanAtlas and in other projects, such as the ICGC Pilots, CPTAC, ICGC-TCGA DREAM Challenges, and the 1000 Genomes SV Project. Here, we demonstrate GenomeVIP's ability to provide high-confidence annotated somatic, germline, and de novo variants of potential biological significance using publicly available data sets.", "claims": [{"id": "claim-method", "statement": "Calculations of true-positive (TP) and false-positive (FP) rates, based on unmasked regions of a known synthetically generated tumor's “truth” set (Ewing et al. 2015), for multiple combinations of parameter sets for the individual, intersected, and combined filtered call sets, is plotted on receiver operating characteristic (ROC) curves (Fig. 4B).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28522612", "locator": "sections[30] \"Somatic\" paragraph 2", "quote": "Calculations of true-positive (TP) and false-positive (FP) rates, based on unmasked regions of a known synthetically generated tumor's “truth” set (Ewing et al. 2015), for multiple combinations of parameter sets for the individual, intersected, and combined filtered call sets, is plotted on receiver operating characteristic (ROC) curves (Fig. 4B)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GenomeVIP source code and associated scripts are freely available for academic use and are available through GitHub (https://github.com/ding-lab/GenomeVIP/) and as Supplemental Code. Users having Amazon Web Services (AWS) login credentials can launch a GenomeVIP server on the AWS cloud by instantiating server images located in the AWS public repository. GenomeVIP executes computations using a public run-time AWS image providing a nearly complete set of the required genomics software. Software packages on these images carry their own licensing and usage terms. For example, GenomeVIP requires users to provide the location of their own licensed copy of GATK (version 3.5 and higher supported). Installation of GenomeVIP on a local web server allows users to design and execute computations on a local high-performance compute cluster using local data or on Amazon's cloud using data stored at AWS; furthermore, GenomeVIP's internal configuration files may be edited manually to point to local versions of the tools on which GenomeVIP depends. GenomeVIP orchestrates many tools that are all upgraded independently, and these updates will be passed through to GenomeVIP users in the following ways: Tool updates not requiring user interface modification will be distributed in updated runtime images, but those requiring such modification will require an updated server image. Tool versions will accumulate rather than be replaced to preserve backward compatibility. Database updates will be managed similarly, although the user can alternatively specify the location of public or custom annotation VCFs that GenomeVIP can retrieve via FTP/HTTP or from Amazon cloud storage. Documentation, support, and further information is available through GitHub and the GenomeVIP home page at our Turnkey Variant Analysis Project website (http://tvap.genome.wustl.edu/tools/genomevip/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28522612", "locator": "sections[32] \"Software availability\" paragraph 2", "quote": "The GenomeVIP source code and associated scripts are freely available for academic use and are available through GitHub (https://github.com/ding-lab/GenomeVIP/) and as Supplemental Code. Users having Amazon Web Services (AWS) login credentials can launch a GenomeVIP server on the AWS cloud by instantiating server images located in the AWS public repository. GenomeVIP executes computations using a public run-time AWS image providing a nearly complete set of the required genomics software. Software packages on these images carry their own licensing and usage terms. For example, GenomeVIP requires users to provide the location of their own licensed copy of GATK (version 3.5 and higher supported). Installation of GenomeVIP on a local web server allows users to design and execute computations on a local high-performance compute cluster using local data or on Amazon's cloud using data stored at AWS; furthermore, GenomeVIP's internal configuration files may be edited manually to point to local versions of the tools on which GenomeVIP depends. GenomeVIP orchestrates many tools that are all upgraded independently, and these updates will be passed through to GenomeVIP users in the following ways: Tool updates not requiring user interface modification will be distributed in updated runtime images, but those requiring such modification will require an updated server image. Tool versions will accumulate rather than be replaced to preserve backward compatibility. Database updates will be managed similarly, although the user can alternatively specify the location of public or custom annotation VCFs that GenomeVIP can retrieve via FTP/HTTP or from Amazon cloud storage. 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Installation of GenomeVIP on a local web server allows users to design and execute computations on a local high-performance compute cluster using local data or on Amazon's cloud using data stored at AWS; furthermore, GenomeVIP's internal configuration files may be edited manually to point to local versions of the tools on which GenomeVIP depends. GenomeVIP orchestrates many tools that are all upgraded independently, and these updates will be passed through to GenomeVIP users in the following ways: Tool updates not requiring user interface modification will be distributed in updated runtime images, but those requiring such modification will require an updated server image. Tool versions will accumulate rather than be replaced to preserve backward compatibility. Database updates will be managed similarly, although the user can alternatively specify the location of public or custom annotation VCFs that GenomeVIP can retrieve via FTP/HTTP or from Amazon cloud storage. 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