1. Efficient population-scale variant analysis and prioritization with VAPr
- Author
-
Guorong Xu, Amanda Birmingham, Adam Mark, Carlo Mazzaferro, and Kathleen M. Fisch
- Subjects
0301 basic medicine ,Statistics and Probability ,Prioritization ,Source code ,Computer science ,media_common.quotation_subject ,Population ,030105 genetics & heredity ,computer.software_genre ,Biochemistry ,03 medical and health sciences ,Exome ,education ,Molecular Biology ,media_common ,computer.programming_language ,education.field_of_study ,Database ,Computational Biology ,Genomics ,Python (programming language) ,Applications Notes ,Computer Science Applications ,Computational Mathematics ,030104 developmental biology ,Computational Theory and Mathematics ,Metagenomics ,computer ,Software - Abstract
Summary With the growing availability of population-scale whole-exome and whole-genome sequencing, demand for reproducible, scalable variant analysis has spread within genomic research communities. To address this need, we introduce the Python package Variant Analysis and Prioritization (VAPr). VAPr leverages existing annotation tools ANNOVAR and MyVariant.info with MongoDB-based flexible storage and filtering functionality. It offers biologists and bioinformatics generalists easy-to-use and scalable analysis and prioritization of genomic variants from large cohort studies. Availability and implementation VAPr is developed in Python and is available for free use and extension under the MIT License. An install package is available on PyPi at https://pypi.python.org/pypi/VAPr, while source code and extensive documentation are on GitHub at https://github.com/ucsd-ccbb/VAPr.
- Published
- 2018