A reference database download link might be outdated or not working

[h171e]

Noticed that the link referenced in the optional step 3. (Optional) Download reference database located in the Getting started page of the read the docs website https://pgsc-calc.readthedocs.io/en/latest/getting-started.html might be referencing an inexistent file or folder.

wget https://ftp.ebi.ac.uk/pub/databases/spot/pgs/resources/pgsc_calc.tar.zst

Checking the directory at https://ftp.ebi.ac.uk/pub/databases/spot/pgs/resources/ made me notice two files that make me wonder if they are required or used by the pipeline with the --run_ancestry parameter and might be needed to be located in the same folder as the reference file.

GRCh38_HAPNEST_reference.tar.zst
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/resources/GRCh38_HAPNEST_reference.tar.zst
GRCh38_HAPNEST_target.tar.zst
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/resources/GRCh38_HAPNEST_target.tar.zst

[nebfield]

Thanks for letting us know! we added HGDP to the reference panel and it looks like some old links are still hiding in the docs.

The best database to use is the combined panel, but it's quite big so we also provide only 1000 Genomes. --run_ancestry only supports one database path.

The HAPNEST databases are smaller synthetic datasets that we use to run automated tests on GitHub Actions and aren't useful when working with real biological data.

I'll dig through the docs and update any old links.