BED (file format)

A BED file consists of a minimum of three columns to which nine optional columns can be added for a total of twelve columns. The first three columns contain the names of chromosomes or scaffolds, the start, and the end coordinates of the sequences considered. The next nine columns contain annotations related to these sequences. These columns must be separated by spaces or tabs, the latter being recommended for reasons of compatibility between programs.[6] Each row of a file must have the same number of columns. The order of the columns must be respected: if columns of high numbers are used, the columns of intermediate numbers must be filled in.

A BED file can optionally contain a header. However, there is no official description of the format of the header. It may contain one or more lines and be signified by different words or symbols,[6] depending on its functional role or simply descriptive. Thus, a header line can begin with these words or symbol:

• "browser": functional header used by the UCSC Genome Browser to set options related to it,
• "track": functional header used by genome browsers to specify display options related to it,
• "#": descriptive header to add comments such as the name of each column.

Unlike the coordinate system used by other standards such as GFF, the system used by the BED format is zero-based for the coordinate start and one-based for the coordinate end.[6] Thus, the nucleotide with the coordinate 1 in a genome will have a value of 0 in column 2 and a value of 1 in column 3.

A thousand-base BED interval with the following start and end:

chr7    0    1000

would convert to the following 1-based "human" genome coordinates, as used by a genome browser such as UCSC:

chr7    1    1000

This choice is justified by the method of calculating the lengths of the genomic regions considered, this calculation being based on the simple subtraction of the end coordinates (column 3) by those of the start (column 2): ${\displaystyle x_{end}-x_{start}}$. When the coordinate system is based on the use of 1 to designate the first position, the calculation becomes slightly more complex: ${\displaystyle x_{end}-x_{start}+1}$. This slight difference can have a relatively large impact in terms of computation time when data sets with several thousand to hundreds of thousands of lines are used.

Alternatively, we can view both coordinates as zero-based, where the end position is non-inclusive. In other words, the zero-based end position denotes the index of the first position after the feature. For the example above, the zero-based end position of 1000 marks the first position after the feature including positions 0 through 999.

Here is a minimal example:

chr7    127471196    127472363
chr7    127472363    127473530
chr7    127473530    127474697

Here is a typical example with nine columns from the UCSC Genome Browser. The first three lines are settings for the UCSC Genome Browser and are unrelated to the data specified in BED format:

browser position chr7:127471196-127495720
browser hide all
track name="ItemRGBDemo" description="Item RGB demonstration" visibility=2 itemRgb="On"
chr7    127471196    127472363    Pos1    0    +    127471196    127472363    255,0,0
chr7    127472363    127473530    Pos2    0    +    127472363    127473530    255,0,0
chr7    127473530    127474697    Pos3    0    +    127473530    127474697    255,0,0
chr7    127474697    127475864    Pos4    0    +    127474697    127475864    255,0,0
chr7    127475864    127477031    Neg1    0    -    127475864    127477031    0,0,255
chr7    127477031    127478198    Neg2    0    -    127477031    127478198    0,0,255
chr7    127478198    127479365    Neg3    0    -    127478198    127479365    0,0,255
chr7    127479365    127480532    Pos5    0    +    127479365    127480532    255,0,0
chr7    127480532    127481699    Neg4    0    -    127480532    127481699    0,0,255