Convert Annotation Track Coordinates

Convert Annotation Track Coordinates converts annotation coordinates, either from hg19 coordinates to hg38 coordinates, or vice versa. This remapping of coordinates, also referred to as 'liftover', makes use of the UCSC Lift Genome Annotations service ( Network access is therefore necessary to use this tool.

The assemblies used for remapping are hg19 (Feb. 2009 (GRCh37/hg19)) and hg38 (Dec. 2013 (GRCh38/hg38)).


The UCSC Lift Genome Annotations service provides a list of options that can be adjusted. Of those, only Minimum ratio of bases that must remap is available in the Convert Annotation Track Coordinates tool. The remaining options are set to default values:

For alternative settings, use the UCSC Lift Genome Annotations service directly. Note that CLC BED import/export, does not support thickStart/thickEnd.

To run Convert Annotation Coordinates Track, go to:

        Toolbox | Biomedical Genomics Analysis (Image biomedical_folder_closed_16_n_p) | Biomedical Utility Tools (Image utilities_closed_16_n_p) | Convert Annotation Track Coordinates (Image convert_coordinates_remap_16_h_p)

The tool takes annotation tracks, typically primer tracks or target region tracks, as input (see figure 6.17).

Image convert_annotation_coordinates_input
Figure 6.17: Selection of a primer annotation track with hg19 coordinates for conversion to hg38 coordinates.

In the next step, a target reference must be selected (see figure 6.18). If the annotation track used as input was based on an hg19 reference, select an hg38 reference genome. If the annotation track used as input was based on an hg38 reference, select an hg19 reference genome. If not already available, a copy of the relevant target reference can be downloaded using the Reference Data Manager.

Image convert_annotation_coordinates_step2
Figure 6.18: This dialog allows selection of the reference sequence you would like to lift over to. Under settings you can choose to adjust the minimum ratio of bases that must remap.

Under settings you can adjust Minimum ratio of bases that must remap. This is the minimum fraction of bases in a region that must be directly aligned in gapless blocks from the first genome to the second.

Convert Annotation Track Coordinates outputs an annotation track containing remapped annotations and a report. The report lists the skipped intervals, that is, the annotations that could not be remapped, together with a comment provided by UCSC (figure 6.19).

Image convert_annotation_coordinates_report
Figure 6.19: The Convert Annotation Track Coordinates report lists skipped intervals.