Cannot reindex from a duplicate axis??

[aglorias]

Hello, I am getting this error and I can't figure out what is the problem. I have compared my files with the format of a file I ran last year successfully, and the only thing I noticed is that in the past, my chromosome names were numeric, while the new vcf have alphanumeric names and periods. Do I need to rename my chromosomes in the vcf?

...conda_envs/locator/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3476, in _can_reindex
raise Value
Error("cannot reindex from a duplicate axis")
ValueError: cannot reindex from a duplicate axis

Any advice is welcome. Attached is the sample file and part of the vcf (had to change .vcf for .txt and cut part of it to be able to upload).
Thanks

Coordinates_AmericaCh.txt
OutAfrica_Chile_noBZ_Sept_2022_gen80m5_locator.txt