Difference between revisions of "Interval format"

Revision as of 16:28, 4 April 2013

The interval format is pretty much like BED format, but only first three columns are well-defined; others can be used for any purpose.

The first three required fields are:

1. chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
2. chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
3. chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.

Other fields (if exist) will be loaded into site properties with names field1, field2 and so on.

Example

Here's an example of track in interval format with additional allele information:

chr22 1000 1001 A C
chr22 1005 1005 - GT
chr22 1010 1012 GC T