📋 PEG Evidence Matrix Standard

Genomic Identifiers

Variant information

Column header	Data format	Description	Requirement	Example data
PrimaryVariantID	chr:bp:ref:alt	Is the variant to which variant-centric evidence relates. Is the primary row ID. Primary variant may be lead variant, variant in LD with lead, or fine mapped SNPs at locus - this should be defined in the metadata file.	Mandatory	chr10:114754071:T:C
rsID	rs[]	The rsID of the primary variant.	Optional	rs1234
Var_[xyz]	Bespoke (Any data type, as long as it is used consistently within the column.)	Other columns relating to variant identification may be added, PEGASUS recommend using the format Var_[xyz] and should be defined in the metadata file.	Optional	bespoke

Gene information

Column header	Data format	Description	Requirement	Example data
GeneID	ENSG[]	The gene under consideration in this row (gene-centric evidence). The Ensembl Gene ID is recommended as the primary identifier. Other IDs can be added using GeneID_[provider] (e.g. GeneID_EntrezID).	Mandatory	ENSG00000151532
GeneSymbol	HGNC	The gene under consideration in this row, to which gene centric evidence relates. HGNC Symbol is recommended as the primary gene symbol identifier. Alternative/legacy symbols may be provided via GeneSymbol_[provider] (e.g. GeneSymbol_alias).	Mandatory	VTI1A
Gene_[xyz]	Bespoke (Any data type, as long as it is used consistently within the column.)	Additional gene-related columns (e.g. Entrez, aliases). Must be defined in metadata.	Optional	Bespoke

Locus information

Column header	Data format	Description	Requirement	Example data
LocusRange	chr:pos:start-end	The range around the primary variant considered in this analysis.	Recommended	chr10:1000-2000
LocusID	Bespoke	An internal or curated ID for the region considered. PEGASUS recommend the associated variant (chr:bp or rsID); internal IDs may be e.g. 'Locus 1, Locus 2'.	Optional	chr10:114754071:T:C
Locus_[xyz]	Bespoke (Any data type, as long as it is used consistently within the column.)	Other columns relating to the locus may be added, PEGASUS recommend using the header format Locus_[xyz], and should be defined in the metadata file.	Optional	bespoke

Evidence — General Pattern

All variant-centric evidence columns are optional. However, PEGASUS suggest to include at least TWO pieces evidence to support variant-gene-phenotype relationship.

PEGASUS define a general reporting pattern:

Column header	Data Format	Description	Requirement	Example data
Category_(stream)_[details]	Bespoke (Any data type, as long as it is used consistently within the column.)	Headers follow the format Category_(stream)_[details]. Category: Use the abbreviated category name from the evidence categories listed in controlled list. (stream) is optional and is only required when multiple evidence streams are used within a single category (e.g. QTL_eqtl). [details] is a user-defined suffix that reflects the content of the data. For any field consisting of multiple words, please use CamelCase. For example, credible set id should be written as CredibleSetID. If no category in the list are applicable, please use Other_[CustomisedCategory]_(stream)_[details]	Optional	variant-centric evidence examples; gene-centric evidence examples

PEGASUS only define column name patterns and does not impose strict requirements on the data type. For guidance, PEGASUS provide reference guidelines for the general evidence categories. Each category — variant-centric, gene-centric, comes with suggested naming patterns and example formats.

Integration Evidence — General Pattern

Column header	Data Format	Description	Requirement	Example data
INT_[tag]_[details]	Bespoke (Any data type, as long as it is used consistently within the column.)	Headers may follow the format INT_[tag]_[details]. INT indicates integration evidence; [tag] is customised label in the metadata; [details] is a user-defined suffix that reflects the content of the data. For multi-word in the [details], use CamelCase (e.g., CombinedPredictionAuthorScore).	Optional	Integration evidence example