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WIG File Format - Definition and supported options

The WIG (wiggle) format is designed for display of dense continuous data such as probability scores. Wiggle data elements must be equally sized; if you need to display continuous data that is sparse or contains elements of varying size, use the BedGraph format instead.

A WIG file consists of one of more blocks, each containing a declaration line followed by lines defining data elements. There are two main formatting options: fixedStep and variableStep.

variableStep

variableStep format is designed for data with irregular intervals between data points, and is the more commonly used format. It begins with a declaration line, followed by two columns containing chromosome positions and data values.

The declaration line begins with the word variableStep and is followed by space-separated key-value pairs:

  • chrom (required) - name of chromosome
  • span (optional, defaults to 1) - the number of bases that each data value should cover

The span allows data to be compressed as follows:

Without span:

variableStep chrom=chr2
300701  12.5
300702  12.5
300703  12.5
300704  12.5
300705  12.5

With span:

variableStep chrom=chr2 span=5
300701  12.5

Both of these examples will display a value of 12.5 at position 300701-300705 on chromosome 2.

fixedStep

fixedStep format is designed for data with regular intervals between data points, and is the more compact of the two wiggle formats. It begins with a declaration line, followed by a single column of data values.

The declaration line begins with the word fixedStep and is followed by space-separated key-value pairs:

  • chrom (required) - name of chromosome
  • start (required) - start point for the data values
  • step (required) - distance between data values
  • span (optional, defaults to 1) - the number of bases that each data value should cover

Without span

fixedStep chrom=chr3 start=400601 step=100
11
22
33

Displays the values 11, 22, 33 as single-base features, on chromosome 3 at positions 400601, 400701 and 400801 respectively.

With span

fixedStep chrom=chr3 start=400601 step=100 span=5
11
22
33

Displays the values 11, 22, 33 as 5-base features, on chromosome 3 at positions 400601-400605, 400701-400705 and 400801-400805 respectively.

Data values

Wiggle element data values can be integer or real, positive or negative. Chromosome positions are 1-relative, i.e. the first base is 1. Only positions specified have data; unspecified positions will be empty.

Track definition lines

Track definition lines can be used to configure the display further. They should be placed at the beginning of the list of data values they are to affect.

The track line consists of the word 'track' followed by space-separated key=value pairs - see the example below. One element is required:

  • type - must be wiggle_0

Valid optional parameters used by Ensembl are:

  • name - unique name to identify this track when parsing the file
  • description - Label to be displayed under the track in Region in Detail
  • priority - integer defining the order in which to display tracks, if multiple tracks are defined.
  • color - as RGB, hex or X11 named color
  • graphType - either 'bar' or 'points'.