How to use a custom scoring file

You might want to use a scoring file that you've developed using different genomic data, or a scoring file somebody else made that isn't published in the PGS Catalog.

Custom scoring files need to follow a specific format. The entire process of using a custom scoring file is described below.

1. Samplesheet setup

First, set up your samplesheet as described here.

2. Scorefile setup

Setup your scorefile in a spreadsheet by concatenating the variant-information to a minimal header in the following format:

#pgs_name=metaGRS_CAD
#pgs_id=metaGRS_CAD
#trait_reported=Coronary artery disease
#genome_build=GRCh37

Variant information should be stored in the following format:

chr_name	chr_position	effect_allele	other_allele	effect_weight
1	2245570	G	C	-2.76009e-02
8	26435271	T	C	1.95432e-02

Save the file as scorefile.txt. The file should be in tab separated values (TSV) format. Column names are defined in the PGS Catalog scoring file format v2.0 and key metadata (e.g. genome_build should be specificied in the header) to ensure variant matching and/or liftover is consistent with the target genotyping data. Scorefiles can be compressed with gzip if you would like to save storage space (e.g. scorefile.txt.gz).

3. Calculate!

Set the path of the custom scoring file with the --scorefile parameter:

$ nextflow run pgscatalog/pgscalc \
    -r v3-alpha.1 \
    -profile <docker/singularity/conda> \
    --input samplesheet.csv \
    --scorefile scorefile.txt

tip

Multiple scoring files can be set using wildcards:

--scorefile path/to/scores/score_*.txt