The Variant Store module extends PhenoTips to support adding pre-processed/annotated genome sequencing data to patient records, filtering variants by annotations and gene-phenotype associations, and allowing for efficient queries across patient records. The default file upload format is a tab-separated file with the following columns:

  • chrom: Chromosome (string)
  • pos: Position (integer, 1-indexed)
  • ref: Reference allele (string)
  • alt: Alternate allele (string)
  • zygosity: "het" or "hom" (string)
  • gene: HGNC gene symbol (string, optional but required for gene-phenotype filtration)

If you are interested the Variant Store being configured to support your custom variant file format or custom annotations, please get in touch with your support contact or send an email to [email protected].

Performance Considerations
As of PhenoTips 6.0, variant store disk usage is approximately 3x that of the original source files (2x is within the attachment store and 1x within the solr index). The variant store should be provided with at least 2 GB of RAM. Indexing speed varies considerably based on the hardware resources, server load, and volume of data in the variant store, but a reasonable estimate is 50 variants / second (so a processed exome file with ~5,000 variants should take 1-2 minutes to index).

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