How to download scoring files from the PGS Catalog¶
pgscatalog-download is a CLI application that makes it easy to download scoring files from the
PGS Catalog with a mixture of PGS, publication, or trait accessions. The application:
automatically retries downloads if they fail
validates the checksum of downloaded scoring files
automatically selects scoring files aligned to a requested genome build
Installation¶
$ pip install pgscatalog-core
Usage¶
Downloading PGS IDs scoring files aligned to GRCh38¶
$ mkdir downloads
$ pgscatalog-download --pgs PGS000822 PGS001229 --build GRCh38 -o downloads
Note
Setting --build will download scoring files harmonised by the PGS Catalog. This means scoring fields have consistent fields, like genomic coordinates.
Downloading all scores associated with a trait¶
To download all scores associated with Alzheimer’s disease:
$ mkdir downloads
$ pgscatalog-download --efo MONDO_0004975 -b GRCh38 -o downloads
By default scores associated with child traits, like late-onset Alzheimer’s disease, are included. To exclude them use:
$ mkdir downloads
$ pgscatalog-download --efo MONDO_0004975 -b GRCh38 -o downloads --efo_direct
Downloading all scores associated with a publication¶
If you’re interested in scores from a specific publication:
$ mkdir downloads
$ pgscatalog-download --pgp PGP000517 -b GRCh38 -o downloads
Help¶
$ pgscatalog-download --help