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How to identify the order of sample IDs in a multi-sample VCF file

Learn how to map patient names to internal sample IDs within downloaded VCF files for Duo, Trio, and extended multi-sample analyses.

After completing a multi-sample analysis, you can download the VCF file from the analysis result page:

When downloading a VCF file from a multi-sample analysis you may notice that the column headers use internal numeric Sample IDs instead of your original patient identifiers. To map these internal IDs back to your specific patients, you can rely on the strict ordering system used during the analysis generation.

The order of the samples in the VCF file depends directly on the type of analysis performed:

  • Duo analyses: The order is always the Mother first, followed by the Father.
  • Trio analyses: The order is always the Proband first, followed by the Mother, and finally the Father.
  • Extended multi-sample analyses: The order of the samples in the VCF file matches the exact order in which the samples were selected when launching the analysis.

Note: This order is also reflected in the analysis name, as well as in the "Coverage", "Allelic Balance", and other columns associated with the samples.