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How to use scoring files in the PGS Catalog

The easiest way to calculate a polygenic score is to use a scoring file that's been published in the PGS Catalog

1. Samplesheet setup​

First, set up your samplesheet as described here.

2. Pick scores from the PGS Catalog​

Accessions​

Individual scores can be used by using Polygenic Score IDs that start with with the prefix PGS. For example, PGS001229. The parameter --pgs_id accepts polygenic score IDs:

 --pgs_id PGS001229

Multiple scores can be set by using a comma separated list:

--pgs_id PGS001229,PGS000802

Traits (phenotypes)​

If you would like to calculate every polygenic score in the Catalog for a trait, like coronary artery disease, then you can use the --efo_id parameter:

--efo_id EFO_0001645

Traits are described using the Experimental Factor Ontology (EFO). Multiple traits can be set by using a comma separated list.

Publications​

If you would like to calculate every polygenic score associated with a publication in the PGS Catalog, you can use the --pgp_id parameter:

--pgp_id PGP000001

Multiple traits can be set by using a comma separated list.

tip

PGS, trait, and publication IDs can be combined to calculate multiple polygenic scores.

3. Calculate!

$ nextflow run pgscatalog/pgscalc \
    -r v3-alpha.1 \
    -profile <docker/singularity/conda> \    
    --input samplesheet.csv \
    --pgs_id PGS001229 \
    --efo_id EFO_0001645 \
    --pgp_id PGP000001