BED

BED File Format

A BED file (.bed) is a tab-delimited text file that defines a feature track. It can have any file extension, but .bed is recommended. The BED file format is described on the UCSC Genome Bioinformatics web site: http://genome.ucsc.edu/FAQ/FAQformat. Tracks in the UCSC Genome Browser (http://genome.ucsc.edu/) can be downloaded to BED files and loaded into IGV.

Notes: 

IGV does not currently support multiple track lines in a single BED file  

Zero-based index: Start and end positions are identified using a zero-based index. The end position is excluded. For example, setting start-end to 1-2 describes exactly one base, the second base in the sequence.

Display settings: To modify IGV's default display settings for the BED data, include a track line in the file.

GFF tag option: By adding a #gffTags line to the beginning of a .bed file, you can add GFF3-style attributes to the Name field (column 4) of a BED file which are displayed in the popup text. 

• The GFF Name property will become the display name of the feature.
• You must URL encode spaces and other whitespace (e.g. replace space with %20).  This is not a requirement of gff3, rather required because bed files are whitespace delimited.

See the GFF3 specification, column 9 for more details.