Make sure that the genome build of the input dataset is specified (click the pencil icon in the history item to set it if necessary).

This tool will only work on interval datasets with chromosome in column 1, start co-ordinate in column 2 and end co-ordinate in column 3. BED comments and track and browser lines will be ignored, but if other non-interval lines are present the tool will return empty output datasets.

What it does

This tool converts coordinates and annotations between assemblies and genomes. It produces 2 files, one containing all the mapped coordinates and the other containing the unmapped coordinates, if any.

Example

Converting the following hg16 intervals to hg18 intervals:

chrX  85170   112199  AK002185  0  +
chrX  110458  112199  AK097346  0  +
chrX  112203  121212  AK074528  0  -

will produce the following hg18 intervals:

chrX  132991  160020  AK002185  0  +
chrX  158279  160020  AK097346  0  +
chrX  160024  169033  AK074528  0  -