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Retrieving reports

Retrieving reports

The Gencove CLI can be used to retrieve various reports on your Gencove data.

Project QC Reports

Quality control data for every completed sample in a given project can be retrieved via the gencove reports project-qc command. The data is returned as a CSV file that is saved locally.

$ gencove reports project-qc --output-filename report.csv <project-id>

You can also select which columns to retrieve via the --columns parameter. By default, all the columns are retrieved. The following columns are supported:

  • id - Gencove sample ID
  • client_id - User supplied ID
  • project_id - Project ID for sample
  • year - Year sample entered completed state
  • month - Month sample entered completed state
  • day - Day sample entered completed state
  • status - Final reported status for sample
  • sex_string - Inferred sex karyotype for sample (if available)
  • snps_min - Minimum number of SNPs detected
  • bases_dedup_mapped_min - Minimum number of deduplicated bases mapped to the target genome
  • call_rate_min - Call rate
  • effective_coverage_min - Effective coverage
  • raw_coverage - Raw coverage
  • ancestries - The ancestry breakdown per sample. This value will be broken down into individual ancestry columns, varying depending on the species for your project pipeline configuration.

Organization Usage Reports

Monthly usage across your entire organization can be retrieved via the gencove reports monthly-usage command. This command downloads a CSV file which reports the number of succeeded and failed samples across all projects, broken down by month.

By default, the previous 12 months are retrieved for the report. A date range can be optionally specified by passing in the --from and --to parameters, both of which expect a date in YYYY-MM format (e.g. 2023-01). Note that the --to parameter is inclusive.

$ gencove reports monthly-usage --from 2023-05 --to 2023-09 --output-filename monthly_usage.csv