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I have a list with nearly 100,000 GPS coordinates in lat/long format in a CSV file. A lot of these are only a few inches away from each other, so I would like to merge them somehow, or filter those out that are too close together within a certain radius.

Do you guys know of a script or a service that can do this automatically?

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There is a reference to a nice paper that explains how to find nearest lat/lng points inside a specified bounding box in another thread, which you can find here: latitude/longitude find nearest latitude/longitude - complex sql or complex calculation

Here is the direct link to the paper: Geo Distance Search with MySQL

I think you can adapt the idea from the paper to your domain in order to set up a filter procedure.