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

Set up a samplesheet as described in: How to set up a samplesheet.

2. Scorefile setup

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

Header:

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

Variant-information:

chr_name	chr_position	effect_allele	other_allele	effect_weight
1	2245570	G	C	-2.76009e-02
8	26435271	T	C	1.95432e-02
10	30287398	C	T	1.82417e-02

Tip

If you’re having trouble getting your scorefile working, see the example we use in our automatic tests

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. Example scorefile templates are available in the calculator repository. Scorefiles can be compressed with gzip if you would like to save storage space (e.g. scorefile.txt.gz).

This how to guide describes a simple scoring file. More complicated scoring files need extra work:

• If you want to set up scoring files to calculate multiple scores in parallel see How to apply multiple scores in parallel

• If you would like to set up a scoring file containing different effect types, see How to set effect type of variants in a scoring file

• If the genome build the custom scoring file was developed with doesn’t match the genome build of the new input genomes, see How to liftover scoring files to match your input genome build

Note

The other_allele column is optional but recommended

3. Calculate!

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

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

Congratulations, you’ve now calculated some scores using your custom scoring file! 🥳

After the workflow executes successfully, the calculated scores and a summary report should be available in the results/ directory by default. If you’re interested in more information, see pgsc_calc Outputs & report.

If the workflow didn’t execute successfully, have a look at the Troubleshooting section.