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PEG List Preparation

This page provides a practical guide to prepare a PEG List for submission or sharing. For the exact column standards, see the PEG List Standard and the toy example.

note

Start from your final PEG Evidence Matrix and the metadata integration tab. The PEG List is derived from the matrix using the integration column marked author_conclusion = True.

Before you start​

Make sure you have:

  • A finalised PEG Evidence Matrix (all evidence and integration columns complete)
  • Only ONE integration column flagged as the author conclusion in metadata
  • The evidence category abbreviations used in the matrix (from the controlled vocabulary)
  • The top gene selection rule for each locus
  • Use a machine-readable table - TSV file
  • Do not use merged cells or styled spreadsheets
  • Headers only contains the evidence category abbreviations (If it other, please use Other_[CustomisedCategory])

List structure​

A PEG List is a compact table where each row represents the top gene at a locus. It should include:

  • A variant identifier (e.g., lead/index variant for the locus)
  • The gene symbol for the author-prioritised gene
  • One column per evidence category (Categories considered in the conclusion, boolean, indicating whether that category was available)
  • The author conclusion integration value (copied from the matrix)

Step-by-step preparation​

1) Start from the Evidence Matrix​

  • Identify the integration column with author_conclusion = True in metadata
  • Use that integration column to determine the top gene per locus
  • If a locus has multiple top genes, include one row per gene and keep the variant identifier

2) Build identifier columns​

  • Use a consistent variant identifier (variant_id or rsID)
  • Use HGNC gene symbols for the Gene symbol column
  • Ensure the genome build and variant format match the matrix

3) Add evidence category columns​

  • Each evidence category abbreviation becomes a boolean column

  • Use a consistent boolean encoding (e.g., TRUE/FALSE)

  • Values indicate whether evidence from that category was available for the author conclusion

  • Ticks do not imply supportive vs negative; they only mean “considered”

4) Add the author conclusion column​

  • Copy the author conclusion integration values from the matrix
  • Use the same header format as the matrix, e.g., INT_CombinedPrediction
  • Ensure the values are consistent with the matrix (same scale and encoding)

Final checks​

  • Variant identifiers and gene symbols are consistent with the matrix
  • Evidence category columns use approved abbreviations
  • The author conclusion column matches the matrix and metadata

If you are unsure about any field or naming pattern, refer back to the PEG List Standard or the PEG Evidence Matrix Preparation guide.