Downloads

PGS Catalog FTP site

This page contains information about the PGS Catalog downloads and FTP.

Available PGS Catalog downloads

PGS Scoring Files & Metadata
Individual PGS variants scoring and metadata files
View PGS Score Directories (FTP)
PGS Catalog Metadata
Available PGS global metadata files
Bulk Metadata Downloads (FTP)
PGS Catalog REST API
Programmatic access to the PGS Catalog metadata
REST API endpoint documentation

PGS Catalog FTP structure

The PGS Catalog FTP allows for consistent access to the bulk downloads, and is indexed by Polygenic Score (PGS) ID to allow programmatic access to score level data. The following diagram illustrates the FTP structure:

ftp://ftp.ebi.ac.uk/pub/databases/spot/pgs
├── pgs_scores_list.txt (list of Polygenic Score IDs)
├── metadata/
│   ├── pgs_all_metadata.xlsx
│   ├── pgs_all_metadata_[sheet_name].csv (7 files)
│   ├── pgs_all_metadata.tar.gz (xlsx + csv files)
│   ├── publications/ (metadata for large studies)
│   └── previous_releases/
└── scores/
  ├── PGS000001/
  │   ├── Metadata/
  │   │   ├── PGS000001_metadata.xlsx
  │   │   ├── PGS000001_metadata_[sheet_name].csv (7 files)
  │   │   ├── PGS000001_metadata.tar.gz (xlsx + csv files)
  │   │   └── archived_versions/
  │   └── ScoringFiles/
  │       ├── PGS000001.txt.gz
  │       └── archived_versions/
  ├── PGS000002/
  ·	├─ ···
  ·	└─ ···
  ·
  └── PGS00XXXX/
      ├─ ···
      └─ ···

PGS Scoring Files

Format: 2.0

Each scoring file (variant information, effect alleles/weights) is formatted to be a gzipped tab-delimited text file, labelled by its PGS Catalog Score ID (e.g. PGS000001.txt.gz). The current PGS

Note: These files are composed of author-reported variants and annotations, and have only been consistently formatted to have the same column headings and data types within each column. We are currently working on methods to provide harmonized versions of each PGS in different genome builds (GRCh37 and GRCh38), ensuring each variant has a chromosomal position (either by adding it based on rsID or using liftover), and flagging potentially problematic variants (e.g. palindromic SNPs) or those that are inconsistent with the current genome build (e.g. strand flips, and variants not found in the Ensembl Variation databases).

PGS Scoring Files Header

Here is a description of the PGS Scoring Files header:

###PGS CATALOG SCORING FILE - see https://www.pgscatalog.org/downloads/#dl_ftp_scoring for additional information
#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 - refers to the EMBL-EBI Terms of Use by default
rsIDchr_namechr_positioneffect_alleleother_alleleeffect_weight...
Note: The "#trait_mapped" and "#trait_efo" metadata can be composed of more than one value (separated by a | "pipe"), e.g.:
#trait_mapped=Ischemic stroke|stroke
#trait_efo=HP_0002140|EFO_0000712
Example of PGS Scoring Files header
###PGS CATALOG SCORING FILE - see https://www.pgscatalog.org/downloads/#dl_ftp_scoring for additional information
#format_version=2.0
##POLYGENIC SCORE (PGS) INFORMATION
#pgs_id=PGS000348
#pgs_name=PRS_PrCa
#trait_reported=Prostate cancer
#trait_mapped=prostate carcinoma
#trait_efo=EFO_0001663
#genome_build=GRCh37
#variants_number=72
#weight_type=log(OR)
##SOURCE INFORMATION
#pgp_id=PGP000113
#citation=Black M et al. Prostate (2020). doi:10.1002/pros.24058
#license=Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0). © 2020 Ambry Genetics.
rsIDchr_namechr_positioneffect_alleleother_alleleeffect_weight...

PGS Scoring Files Columns

It also has been edited to have consistent column headings based on the following schema:

Column HeaderField NameField RequirementField Description
Variant Description:
rsIDdbSNP Accession ID (rsID)Optional The SNP’s rs ID.
This column also contains HLA alleles in the standard notation (e.g. HLA-DQA1*0102) that aren’t always provided with chromosomal positions.
chr_nameLocation - Chromosome Required Chromosome name/number associated with the variant
chr_positionLocation - Position within the ChromosomeRequired Chromosomal position associated with the variant
effect_alleleEffect AlleleRequiredThe allele that's dosage is counted (e.g. {0, 1, 2}) and multiplied by the variant's weight (effect_weight) when calculating score. The effect allele is also known as the 'risk allele'.
other_alleleOther allele(s)Recommended The other allele(s) at the loci
locus_nameLocus NameOptionalThis is kept in for loci where the variant may be referenced by the gene (APOE e4). It is also common (usually in smaller PGS) to see the variants named according to the genes they impact.
is_haplotype
is_diplotype
FLAG: Haplotype or DiplotypeOptionalThis is a TRUE/FALSE variable that flags whether the effect allele is a haplotype/diplotype rather than a single SNP. Constituent SNPs in the haplotype are semi-colon separated.
imputation_methodImputation MethodOptionalThis described whether the variant was specifically called with a specific imputation or variant calling method. This is mostly kept to describe HLA-genotyping methods (e.g. flag SNP2HLA, HLA*IMP) that gives alleles that are not referenced by genomic position.
variant_descriptionVariant DescriptionOptionalThis field describes any extra information about the variant (e.g. how it is genotyped or scored) that cannot be captured by the other fields.
inclusion_criteriaScore Inclusion CriteriaOptionalExplanation of when this variant gets included into the PGS (e.g. if it depends on the results from other variants).
Weight Information:
effect_weightVariant WeightRequiredValue of the effect that is multiplied by the dosage of the effect allele (effect_allele) when calculating the score. Additional information on how the effect_weight was derived is in the weight_type field of the header, and score development method in the metadata downloads.
is_interactionFLAG: InteractionOptionalThis is a TRUE/FALSE variable that flags whether the weight should be multiplied with the dosage of more than one variant. Interactions are demarcated with a _x_ between entries for each of the variants present in the interaction.
is_dominantFLAG: Dominant Inheritance ModelOptionalThis is a TRUE/FALSE variable that flags whether the weight should be added to the PGS sum if there is at least 1 copy of the effect allele (e.g. it is a dominant allele).
is_recessiveFLAG: Recessive Inheritance ModelOptionalThis is a TRUE/FALSE variable that flags whether the weight should be added to the PGS sum only if there are 2 copies of the effect allele (e.g. it is a recessive allele).
dosage_0_weightEffect weight with 0 copy of the effect alleleOptionalWeights that are specific to different dosages of the effect_allele (e.g. {0, 1, 2} copies) can also be reported when the the contribution of the variants to the score is not encoded as additive, dominant, or recessive. In this case three columns are added corresponding to which variant weight should be applied for each dosage, where the column name is formated as dosage_#_weight where the # sign indicates the number of effect_allele copies.
dosage_1_weightEffect weight with 1 copy of the effect alleleOptional
dosage_2_weightEffect weight with 2 copies of the effect alleleOptional
Other information:
OR
HR
Odds Ratio [OR], Hazard Ratio [HR]OptionalAuthor-reported effect sizes can be supplied to the Catalog. If no other effect_weight is given the weight is calculated using the log(OR) or log(HR).
allelefrequency_effectEffect Allele FrequencyOptionalReported effect allele frequency, if the associated locus is a haplotype then haplotype frequency will be extracted.
allelefrequency_effect_AncestryPopulation-specific effect allele frequencyOptionalReported effect allele frequency in a specific population (described by the authors).
Example of PGS Scoring Files data
Scoring Files header
rsID        chr_name  chr_position  effect_allele  other_allele  effect_weight
rs2843152   1         2245570       G              C             -2.76009e-02
rs35465346  1         22132518      G              A             2.39340e-02
rs28470722  1         38386727      G              A             -1.74935e-02
rs11206510  1         55496039      T              C             2.93005e-02
rs9970807   1         56965664      C              T             4.70027e-02
rs61772626  1         57015668      A              G             -2.71202e-02
rs7528419   1         109817192     A              G             2.91912e-02
rs1277930   1         109822143     A              G             2.60105e-02
rs11102000  1         110298166     G              C             2.45969e-02
rs11810571  1         151762308     G              C             2.09215e-02
rs6689306   1         154395946     G              A             -1.97906e-02
rs72702224  1         154911689     G              A             -2.81310e-02
rs3738591   1         155764808     C              G             4.23731e-02
...

PGS Scoring Files Format changes

PGS Scoring Files Previous formats

PGS Catalog Metadata

Bulk download of the entire PGS Catalog's metadata, describing all PGS in terms of their publication source, samples used for development/evaluation, and related performance metrics. Download Metadata file.xlsx

The bulk download contains a single Excel file with multiple sheets describing each of the data types. The sheets are also provided as individual .csv files for easier import in analysis tools, and are provided on the FTP in the metadata/ folder.

Worksheet Description Download Sheet.csv
ReadmePGS Catalog Release Date and Summary Information.-
PublicationsLists the publication sources for the PGS and PGS evaluations in the catalog.
EFO TraitsLists the ontology-mapped traits information for all PGS in the catalog.
ScoresLists all PGS scores and their associated metadata.
Score Development SamplesLists the samples used to create the PGS: samples used to discover the variant associations (GWAS), samples used for score development/training.
Performance MetricsLists all performance metrics and the associated PGS Scores and Publications.
Evaluation Sample SetsDescribes the samples used to evaluate PGS performance (refferenced as Polygenic Score Sample Sets (PSS).
CohortsLists all the cohorts used in the different samples.