Notice: Upcoming Changes to the Scoring File Format

Download an example in the new format: PGS000001

Dear users, we wanted to update you on some upcoming minor changes we will be making to the PGS Catalog scoring files on December 15, 2021. The changes will be applied to all scores, and previously curated scores will be updated to the new format. The changes will make the metadata in the header more complete and easier to parse, and to make it slightly more compact. The changes are as follows:

We hope this doesn’t cause our users much of an inconvenience, the older versions of the scoring files will still be provided in the archived data directories of each score in the PGS Catalog FTP. If you have any questions or comments about the changes please get in touch with us by e-mail at pgs-info@ebi.ac.uk. You can find a visual guide to the changes to the header below:

New format [version 2.0]
###PGS CATALOG SCORING FILE - see ...
#format_version=Version of the scoring file format, e.g. '2.0'
##POLYGENIC SCORE (PGS) INFORMATION
#pgs_id=PGS identifier, e.g. 'PGS000001'
#pgs_name=PGS name, e.g. 'PRS77_BC' - optional
#trait_reported=trait, e.g. 'Breast Cancer'
#trait_mapped=Ontology trait name, e.g. 'breast carcinoma'
#trait_efo=Ontology trait ID (EFO), e.g. 'EFO_0000305'
#genome_build=Genome build/assembly, e.g. 'GRCh38'
#variants_number=Number of variants listed in the PGS
#weight_type=Variant weight type, e.g. 'beta', 'OR/HR' (default 'NR')
##SOURCE INFORMATION
#pgp_id=PGS publication identifier, e.g. 'PGP000001'
#citation=Information about the publication
#license=License and terms of PGS use/distribution ...
rsIDchr_namechr_positioneffect_alleleother_allele...
Current format [version 1.0]
### PGS CATALOG SCORING FILE - see ...

## POLYGENIC SCORE (PGS) INFORMATION
# PGS ID = PGS identifier, e.g. 'PGS000001'
# PGS Name = PGS name, e.g. 'PRS77_BC' - optional
# Reported Trait = trait, e.g. 'Breast Cancer'


# Original Genome Build = Genome build/assembly, e.g. 'GRCh38'
# Number of Variants = Number of variants listed in the PGS

## SOURCE INFORMATION
# PGP ID = PGS publication identifier, e.g. 'PGP000001'
# Citation = Information about the publication
# LICENSE = License and terms of PGS use/distribution ...
rsIDchr_namechr_positioneffect_allelereference_allele...