GenomeVIP: A cloud platform for genomic variant discovery and interpretation

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

Research output: Contribution to journalArticle

9 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)1450-1459
Number of pages10
JournalGenome Research
Volume27
Issue number8
DOIs
StatePublished - Aug 2017

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

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  • Cite this

    Mashl, R. J., Scott, A. D., Huang, K. L., Wyczalkowski, M. A., Yoon, C. J., Niu, B., DeNardo, E., Yellapantula, V. D., Handsaker, R. E., Chen, K., Koboldt, D. C., Ye, K., Fenyö, D., Raphael, B. J., Wendl, M. C., & Ding, L. (2017). GenomeVIP: A cloud platform for genomic variant discovery and interpretation. Genome Research, 27(8), 1450-1459. https://doi.org/10.1101/gr.211656.116