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Update FTP links
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nebfield authored Oct 3, 2023
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16 changes: 11 additions & 5 deletions docs/how-to/ancestry.rst
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Expand Up @@ -6,17 +6,23 @@ How do I normalise calculated scores across different genetic ancestry groups?
Download reference data
-----------------------

The fastest method of getting started is to download our reference panel:
The fastest method of getting started is to download a `reference panel`_:

.. code-block:: console
$ wget https://ftp.ebi.ac.uk/pub/databases/spot/pgs/resources/pgsc_calc.tar.zst
$ wget https://ftp.ebi.ac.uk/pub/databases/spot/pgs/resources/pgsc_1000G_v1.tar.zst
The reference panel is based on 1000 Genomes. It was originally downloaded from
the PLINK 2 `resources section`_. To minimise file size INFO annotations are
excluded. KING pedigree corrections were enabled.
This example reference panel is based on 1000 Genomes.

We also provide a reference panel that includes Human Genome Diversity Project data,
which includes more ancestry groups:

.. code-block:: console
$ wget https://ftp.ebi.ac.uk/pub/databases/spot/pgs/resources/pgsc_HGDP+1kGP_v1.tar.zst
.. _`resources section`: https://www.cog-genomics.org/plink/2.0/resources
.. _`reference panel`: https://ftp.ebi.ac.uk/pub/databases/spot/pgs/resources/

Bootstrap reference data
~~~~~~~~~~~~~~~~~~~~~~~~
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