I added a large file to a git repository (102Mb), commited and push and got an error due to size limit limitations on github
remote: error: GH001: Large files detected. You may want to try Git Large File Storage - https://git-lfs.github.com.
remote: error: Trace: 7d51855d4f834a90c5a5a526e93d2668
remote: error: See http://git.io/iEPt8g for more information.
remote: error: File coverage/sensitivity/simulated.bed is 102.00 MB; this exceeds GitHub's file size limit of 100.00 MB
Here, you see the path of the file (coverage/sensitivity/simualted.bed).
So, the solution is actually quite simple (when you know it): you can use the filter-branch command as follows:
git filter-branch --tree-filter 'rm -rf path/to/your/file' HEAD git push