Table 8 The time consumptions (in seconds) of BEDTools and BEDOPS for coarse interval intersection query compared with RTFC.

From: Efficient Genomic Interval Queries Using Augmented Range Trees

Tools

BEDTools

BEDOPS*

RTFC

sort

query

total

build

query

total

Time consumption

126911.72

2111.65

2388.56

4500.21

6971.58

1825.82

8797.40

  1. The data intervals are ENCODE intervals and query intervals are gnomAD intervals. *BEDOPS cannot return the detailed intersection information as RTFC and BEDTools, it returns only the subset of overlapping intervals in the first bed file and ignores the overlapping intervals in the second bed file.
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