VAS: a convenient web portal for efficient integration of genomic features with millions of genetic variants

BMC Genomics

Table 2 Data integration time of different methods

Method	Integrating variant	Integrating variant flanking
	locations (second)	windows (second)
BigBed	277.90	275.63
Interval tree	0.41	0.60
Relational database	8.05	736.23
Tabix	8.87	8.88
Our algorithms	0.21	0.52

For BigBed reader and interval tree, we used the implementation of bxpython. For relational database, we tried several indexing methods including standard B-tree index and spatial index, and report here the shortest time among these approaches. Tabix was called using the pytabix library in Python.

ISSN: 1471-2164