between assemblies and genomesliftOver_wrapper.py $input "$out_file1" "$out_file2" $dbkey $to_dbkey $minMatchucsc_tools
.. class:: warningmark
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).
.. class:: warningmark
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.
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.. class:: infomark
**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.
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**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 -