PGS Catalog - Download Information

Downloads

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
Python package pgscatalog_utils A collection of tools, such as scoring files download	Python package 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/
        │           └── Harmonized/
        │                 ├── PGS000001_hmPOS_GRCh37.txt.gz
        │                 └── PGS000001_hmPOS_GRCh38.txt.gz
        ├── PGS000002/
        ·     ├─ ···
        ·     └─ ···
        ·
        └── PGS00XXXX/
              ├─ ···
              └─ ···

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
Readme	PGS Catalog Release Date and Summary Information.	-
Publications	Lists the publication sources for the PGS and PGS evaluations in the catalog.
EFO Traits	Lists the ontology-mapped traits information for all PGS in the catalog.
Scores	Lists all PGS scores and their associated metadata.
Score Development Samples	Lists the samples used to create the PGS: samples used to discover the variant associations (GWAS), samples used for score development/training.
Performance Metrics	Lists all performance metrics and the associated PGS Scores and Publications.
Evaluation Sample Sets	Describes the samples used to evaluate PGS performance (refferenced as Polygenic Score Sample Sets (PSS).
Cohorts	Lists all the cohorts used in the different samples.

PGS Scoring Files

Formatted Files

Format: 2.0

Header— Columns— Format changes— Previous formats

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).

They can be found in URLs like this:

ftp://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS######/ScoringFiles/

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).

Formatted 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...

Formatted Files — Columns

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

Column Header	Field Name	Field Requirement	Field Description
Variant Description:
rsID	dbSNP 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_name	Location - Chromosome	Required	Chromosome name/number associated with the variant
chr_position	Location within the Chromosome	Required	Chromosomal position associated with the variant
effect_allele	Effect Allele	Required	The 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_allele	Other allele(s)	Recommended	The other allele(s) at the loci
locus_name	Locus Name	Optional	This 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 Diplotype	Optional	This 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_method	Imputation Method	Optional	This 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_description	Variant Description	Optional	This 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_criteria	Score Inclusion Criteria	Optional	Explanation of when this variant gets included into the PGS (e.g. if it depends on the results from other variants).
Weight Information:
effect_weight	Variant Weight	Required	Value 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_interaction	FLAG: Interaction	Optional	This 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_dominant	FLAG: Dominant Inheritance Model	Optional	This 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_recessive	FLAG: Recessive Inheritance Model	Optional	This 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_weight	Effect weight with 0 copy of the effect allele	Optional	Weights 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_weight	Effect weight with 1 copy of the effect allele	Optional
dosage_2_weight	Effect weight with 2 copies of the effect allele	Optional
Other information:
OR HR	Odds Ratio [OR], Hazard Ratio [HR]	Optional	Author-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_effect	Effect Allele Frequency	Optional	Reported effect allele frequency, if the associated locus is a haplotype then haplotype frequency will be extracted.
allelefrequency_effect_Ancestry	Population-specific effect allele frequency	Optional	Reported 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
...

Formatted Files — Format changes

Version 2.0
- Header (metadata)
  - The metadata labels will change from the previous text-based titles to new field labels that match the outputs of the REST API Score and Publication endpoints. We will also adopt new formatting by removing spaces (e.g. 'PGS ID' is changed to 'pgs_id').
    This should make the data easier to parse and more consistent across methods of data access.
  - Addition of the #format_version field.
    New versioning to keep track of the format changes.
  - Addition of the new metadata fields #trait_mapped and #trait_efo.
    These fields should make it easier to group scores based on structured trait terms.
  - Addition of the #weight_type field.
    This information was previously included as a column in the scoring file. This lets users know how the effect_weight column was derived (if known), otherwise it is labeled as NR (Not Reported).
- Scoring File Schema (Column data)
  - Move redundant information of the column weight_type into the header.
    In all cases the weight_type was identical across all variants in a score. To remove redundant columns with identical data we moved this information into a metadata field that is now presented on the website and API as well as in the scoring file header.
  - Rename the column reference_allele to other_allele.
    We are renaming this column other_allele to remove the use of the word "reference". "Reference allele" may have been confused with the allele included in the reference genome assembly. The other/non-effect allele may or may not be the reference genome allele. Initially we had named it reference_allele to refer to the allele that when homozygous has zero (reference) dosage. We now rename it other_allele to reflect that it is the non-effect allele. This terminology is consistent with the GWAS summary statistics standard format used by the GWAS Catalog.
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...
Schema 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...
- New header information
- Column name change

Formatted Files — Previous formats

Version 1.0 (up to December 14, 2021)

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
## 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 - refers to the EMBL-EBI Terms of Use by default
rsIDchr_namechr_positioneffect_allelereference_allele...

Example of PGS Scoring Files header

### PGS CATALOG SCORING FILE - see https://www.pgscatalog.org/downloads/#dl_ftp_scoring for additional information
## POLYGENIC SCORE (PGS) INFORMATION
# PGS ID = PGS000348
# PGS Name = PRS_PrCa
# Reported Trait = Prostate cancer
# Original Genome Build = GRCh37
# Number of Variants = 72
## 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_allelereference_alleleeffect_weight...

Columns

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

Column Header	Field Name	Field Description	Field Requirement
rsID	dbSNP Accession ID (rsID)	The SNP’s rs ID	Optional - unless both the chr_name and chr_position columns are absent. This column also contains HLA alleles in the standard notation (e.g. HLA-DQA1*0102) that aren’t always provided with chromosomal positions.
chr_name	Location - Chromosome	Chromosome name/number associated with the variant	Required - may be optional if an rsID for the variant is provided
chr_position	Location within the Chromosome	Chromosomal position associated with the variant	Required - may be optional if an rsID for the variant is provided
effect_allele	Effect Allele	The 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'.	Required
reference_allele	Reference Allele	The other allele(s) at the loci	Optional - but strongly recommended
effect_weight	Variant Weight	Value of the effect that is multiplied by the dosage of the effect allele ('effect_allele') when calculating the score.	Required
locus_name	Locus Name	This 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.	Optional
weight_type	Type of Weight	Whether the author supplied Variant Weight is a: beta (effect size), or something like an OR/HR (odds/hazard ratio)	Optional
allelefrequency_effect	Effect Allele Frequency	Reported effect allele frequency, if the associated locus is a haplotype then haplotype frequency will be extracted.	Optional
is_interaction	FLAG: Interaction	This 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.	Optional
is_dominant	FLAG: Dominant Inheritance Model	This 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).	Optional
is_recessive	FLAG: Recessive Inheritance Model	This 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).	Optional
is_haplotype is_diplotype	FLAG: Haplotype or Diplotype	This 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.	Optional
imputation_method	Imputation Method	This 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.	Optional
variant_description	Variant Description	This field describes any extra information about the variant (e.g. how it is genotyped or scored) that cannot be captured by the other fields.	Optional
inclusion_criteria	Score Inclusion Criteria	Explanation of when this variant gets included into the PGS (e.g. if it depends on the results from other variants).	Optional
Extra columns:
OR HR	Odds Ratio [OR], Hazard Ratio [HR]	Author-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).	Optional
allelefrequency_effect_Ancestry	Population-specific effect allele frequency	Reported effect allele frequency in a specific population (described by the authors).	Optional

Example of PGS Scoring Files data

Scoring Files header
rsID        chr_name  chr_position  effect_allele  reference_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
...

Harmonized Files

Format: 2.0

File name— Header— Additional Columns

PGS Scoring Files in the Catalog are currently provided in a consistent format with standardized column names and data types, along with information about the genome build given by authors. The variant-level information in PGS is often heterogeneously described and may lack chromosome/position information, contain a mix of positions and/or rsIDs, or be mapped to a genome build different from your sample genotypes. To make PGS easier to apply we have created a new set of files that contain additional columns with harmonized variant information (chromosome name and base pair position) and variant identifiers (updated rsID), in commonly used genome builds (GRCh37/hg19 and GRCh38/hg38) to make variant matching and PGS calculation easier.

The generation of these harmonized files is done by using the pgs-harmonizer tool. It is based on the Open Targets and GWAS Catalog Summary Statistics harmonizer pipelines. To harmonize the variant positions the pgs-harmonizer performs the following tasks:

Mapping rsIDs to chromosomal positions: we use Ensembl (VCF files and REST APIs) on GRCh37 and GRCh38. We use Ensembl version 105.
Liftover - mapping chromosomal positions across builds (only when generating a Scoring file on a different genome build): we use the UCSC liftover tools via the Python library pyliftover.

The resultant files create new columns, indicating the source of the variant annotation (hm_source), as well as consistently annotated chromosome (hm_chr) / position (hm_pos), and rsID (hm_rsID) which can be used to match variants in your dataset along with the alleles (effect_allele, and other_allele).

Warning: Complex variants in the human leukocyte antigen (HLA) region (alleles/haplotypes/diplotypes) and larger copy number variants (CNVs) without explicit positions will have missing harmonized positions as they are not indexed in the ENSEMBL VCFs. For these variants we suggest using the author-reported annotations, specifically the effect_allele column, for variant matching in absence of positional information.

Harmonized scoring files can be accessed via our FTP, in a separate directory for each score:

ftp://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS######/ScoringFiles/Harmonized/

Note: The harmonized scoring file URLs can also be found for any Score result within the REST API.

Harmonized Files — File name

The file name is composed of 3 parts, separated by underscores (_):

PGS ID, e.g. 'PGS000001'
Type of harmonized file, e.g. 'hmPOS'
Genome build, either 'GRCh37' or ‘GRCh38’

For instance: PGS000001_hmPOS_GRCh37.txt.gz

Harmonized Files — Header

Note: The first part of the header (before the line ##HARMONIZATION DETAILS) is a copy-paste of the Scoring file header.

Here is a description of the PGS Harmonized 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'
...
#license=License and terms of PGS use/distribution - refers to the EMBL-EBI Terms of Use by default
##HARMONIZATION DETAILS
#HmPOS_build=Genome build of the harmonized file, e.g. 'GRCh38'
#HmPOS_date=Date of the harmonized file creation, e.g. '2022-05-26'
#HmPOS_match_chr=Number of entries matching and not matching the given chromosome, e.g. {"True": 5210, "False": 8}
#HmPOS_match_pos=Number of entries matching and not matching the given position, e.g. {"True": 5210, "False": 8}
rsID...hm_sourcehm_rsIDhm_chrhm_poshm_inferOtherAllelehm_match_chrhm_match_pos

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
...
#license=Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0). © 2020 Ambry Genetics.
##HARMONIZATION DETAILS
#HmPOS_build=GRCh37
#HmPOS_date=2022-07-26
#HmPOS_match_chr={"True": 72, "False":0}
#HmPOS_match_pos={"True": 72, "False":0}
rsID...hm_sourcehm_rsIDhm_chrhm_poshm_inferOtherAllelehm_match_chrhm_match_pos

Harmonized Files — Additional Columns

The formatted scoring file (in the original genome build) has the following additional columns describing the variants in the specified genome build for each HmPOS file:

Additional Column Header	Field Name	Field Description
hm_source	Provider of the harmonized variant information	Data source of the variant position. Options include: ENSEMBL, liftover, author-reported (if being harmonized to the same build).
hm_rsID	Harmonized rsID	Current rsID. Differences between this column and the author-reported column (rsID) indicate variant merges and annotation updates from dbSNP.
hm_chr	Harmonized chromosome name	Chromosome that the harmonized variant is present on, preferring matches to chromosomes over patches present in later builds.
hm_pos	Harmonized chromosome position	Chromosomal position (base pair location) where the variant is located, preferring matches to chromosomes over patches present in later builds.
hm_inferOtherAllele	Harmonized other alleles	If only the effect_allele is given we attempt to infer the non-effect/other allele(s) using Ensembl/dbSNP alleles.
hm_match_chr	FLAG: matching chromosome name	Used for QC. Only provided if the scoring file is being harmonized to the same genome build, and where the chromosome name is provided in the column chr_name.
hm_match_pos	FLAG: matching chromosome position	Used for QC. Only provided if the scoring file is being harmonized to the same genome build, and where the chromosome name is provided in the column chr_position.

Example of PGS Harmonized File (GRCh37 file harmonized on GRCh38)

###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=PGS000116
...
#genome_build=GRCh37
...
##HARMONIZATION DETAILS
#HmPOS_build=GRCh38
...
rsID         chr_name  chr_position  effect_allele  other_allele  effect_weight  hm_source  hm_rsID      hm_chr  hm_pos
rs1921       1          949608       A              G             -0.003965      ENSEMBL    rs1921       1       1014228
rs2710887    1          986443       T              C             -0.000846      ENSEMBL    rs2710887    1       1051063
rs11260596   1         1002434       T              C              0.000789      ENSEMBL    rs11260596   1       1067054
rs113355263  1         1069535       A              G             -0.001627      ENSEMBL    rs113355263  1       1134155
rs11260539   1         1109903       T              C              0.000170      ENSEMBL    rs11260539   1       1174523
...

Downloads

Available PGS Catalog downloads

PGS Catalog FTP structure

PGS Catalog Metadata

PGS Scoring Files

Formatted Files

Formatted Files — Header

Formatted Files — Columns

Formatted Files — Format changes

Format version 2.0

Schema version 1.0

Formatted Files — Previous formats

Header

Columns

Harmonized Files

Harmonized Files — File name

Harmonized Files — Header

Harmonized Files — Additional Columns