Lift-over coordinates from one reference genome version to another

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Locally and confidentially

You can lift over coordinates using the Jim Kent liftover tool. Download it from

  • liftOver but keep header track line (from IGV track file)
sed -e "s/^track /#track /; s/^browser /#browser/" customTrackBedFile.txt \
	| liftOver stdin map.chain stdout unMapped \
	| sed -e "s/^#track/track/; s/^#browser/browser/" > liftedCustomTrackBedFile.txt

See also:

On the web

Two places are available for web-gui liftOver