Matching genomic regions / Merge BED

Description

Merges overlapping regions (features) in one BED/GFF/VCF file into a single interval.

Parameters

• Force strandedness (yes, no) [no]
• Report the number of features that were merged (yes, no) [no]
• Maximum distance between features allowed (Integer) [0]
• Report the names of the merged features separated by semicolons (yes, no) [no]
• Report the scores of the merged features (yes, no) [no]
• Score report type (sum, min, max, mean, median, mode, antimode, collapse) [sum]

Details

This tool combines overlapping or “book-ended” (that is, one base pair away) features in a feature file into a single feature which spans all of the combined features.

Output

Output is a BED file.

References

This tool uses the BEDTools package. Please cite the article:

Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.

Please see the BEDTools homepage for more details.