TY  - JOUR
A1  - Huang, Dandan
A1  - Yi, Xianfu
A1  - Zhou, Yao
A1  - Yao, Hongcheng
A1  - Xu, Hang
A1  - Wang, Jianhua
A1  - Zhang, Shijie
A1  - Nong, Wenyan
A1  - Wang, Panwen
A1  - Shi, Lei
A1  - Xuan, Chenghao
A1  - Li, Miaoxin
A1  - Wang, Junwen
A1  - Li, Weidong
A1  - Kwan, Hoi Shan
A1  - Sham, Pak Chung
A1  - Wang, Kai
A1  - Li, Mulin Jun
T1  - Ultrafast and scalable variant annotation and prioritization with big functional genomics data
Y1  - 2020/12/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1789 
EP  - 1801 
DO  - 10.1101/gr.267997.120 
VL  - 30 
IS  - 12 
UR  - http://genome.cshlp.org/content/30/12/1789.abstract 
N2  - The advances of large-scale genomics studies have enabled compilation of cell type–specific, genome-wide DNA functional elements at high resolution. With the growing volume of functional annotation data and sequencing variants, existing variant annotation algorithms lack the efficiency and scalability to process big genomic data, particularly when annotating whole-genome sequencing variants against a huge database with billions of genomic features. Here, we develop VarNote to rapidly annotate genome-scale variants in large and complex functional annotation resources. Equipped with a novel index system and a parallel random-sweep searching algorithm, VarNote shows substantial performance improvements (two to three orders of magnitude) over existing algorithms at different scales. It supports both region-based and allele-specific annotations and introduces advanced functions for the flexible extraction of annotations. By integrating massive base-wise and context-dependent annotations in the VarNote framework, we introduce three efficient and accurate pipelines to prioritize the causal regulatory variants for common diseases, Mendelian disorders, and cancers. 
ER  -