vcf-dimensions.md

VCF Dimensions caching

TODO

This a prerequisite step before running any queries

The dimensions update job will:

• For each VCF files in the project data store:
  • store filename and data store file version ID
  • store timestamp of last update [TODO IS THIS LAST TIME DIMENSIONS WAS RUN OR LAST TIME FILE WAS UPDATED?]
  • Fetche and store all sample names from the VCF file
  • Fetch and store all chromosome/scaffold/contig names
  • count the number of samples and variants in the VCF file
• not consider results files produced by DivBase
  • by filename (result_of_job_ prefix)
  • as an additional check, looks for bcftools annotate stamp in header (all DivBase results files are branded like this)

Run divbase-cli dimensions update whenever:

• A new VCF file is uploaded to the project
• A new version of an existing VCF file is uploaded to the project