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 NCBI Remapping Service (https://www.ncbi.nlm.nih.gov/genome/tools/remap). Network access is therefore necessary to use this tool.
To run Convert Annotation Coordinates Track, go to:
Tools | QIAseq Panel Expert Tools (
) | QIAseq DNA Panel Expert Tools (
) | Convert Annotation Track Coordinates (
)
The tool takes annotation tracks, typically primer tracks or target region tracks, as input (see figure 5.26).
Figure 5.26: Selection of a primer annotation track with hg19 coordinates for coversion to hg38 coordinates.
In the next step, a target reference must be selected. 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.
This tool outputs an annotation track with coordinates based on the target reference, and a report that lists the skipped intervals, that is, the annotations that could not be mapped to coordinates of the selected target reference (see figure 5.27).
Figure 5.27: The Convert Annotation Track Coordinates report lists the skipped intervals.