Ploidy

The Ploidy column displays results from the DRAGEN Ploidy Estimator, which detects aneuploidies and infers the sex karyotype in whole genome cases.

Ploidy values are derived from the *.ploidy_estimation_metrics.csv DRAGEN output file.

Ploidy estimation results

Pass

• All autosomes fall within the expected ploidy range. No large‑scale autosomal copy number deviation is detected.

Fail

• At least one autosome has a median ploidy score below 0.9 or above 1.1. Hover over the result to see which chromosomes are problematic.

N/A

• Ploidy metrics are not available.

Best practices

• Check ploidy early in case review to quickly identify potential large‑scale chromosomal abnormalities.

• Verify sex karyotype by confirming whether the sex karyotype inferred from ploidy matches the sex validation results to rule out sample swaps.

• A failed ploidy result does not confirm a clinical abnormality. It indicates aberrant copy number estimation and must be interpreted in the context of other QC metrics and genomic visualization.

Ploidy availability by workflow

Ploidy evaluation in the Lab tab is available only for whole genome FASTQ cases.

In whole genome FASTQ cases, ploidy is shown in both the DRAGEN QC report and the Lab tab. The DRAGEN pipeline automatically generates the *.ploidy_estimation_metrics.csv file, which the platform uses to display ploidy results. Under this workflow, ploidy appears consistently across the interface.

In whole genome Bring your own DRAGEN (BYOD) VCF cases, ploidy is shown only in the DRAGEN QC report, never in the Lab tab. When a case is created from VCF, the DRAGEN metrics supplied in a *.metrics.tar.gz archive are used exclusively to generate the DRAGEN report and are not ingested into the Lab tab. The platform displays N/A for Ploidy in the Lab tab.