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Open Access Technical Note

VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern

Qiang Hu1, Dan Wang1, Li Yan1, Hua Zhao2 and Song Liu1*

Author Affiliations

1 Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, New York 14263, USA

2 Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York 14263, USA

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BMC Research Notes 2012, 5:31  doi:10.1186/1756-0500-5-31

Published: 14 January 2012



The massive amounts of genetic variant generated by the next generation sequencing systems demand the development of effective computational tools for variant prioritization.


VPA (Variant Pattern Analyzer) is an R tool for prioritizing variants with specified frequency pattern from multiple study subjects in next-generation sequencing study. The tool starts from individual files of variant and sequence calls and extract variants with user-specified frequency pattern across the study subjects of interest. Several position level quality criteria can be incorporated into the variant extraction. It can be used in studies with matched pair design as well as studies with multiple groups of subjects.


VPA can be used as an automatic pipeline to prioritize variants for further functional exploration and hypothesis generation. The package is implemented in the R language and is freely available from webcite.