> For the complete documentation index, see [llms.txt](https://help.dragen.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/germline/standard-sbs/ploidy_estimator_accuracy.md).

# WGS Ploidy Estimator

Generated on **2026-05-07**

## Ploidy Estimator

The Ploidy Estimator uses reads from the mapper/aligner to calculate the sequencing depth of coverage for each autosome and allosome in the human genome. The sex karyotype of the sample is then estimated using the ratios of the median sex chromosome coverages to the median autosomal coverage. The sex karyotype is estimated based on the range the ratios fall in. If the ratios are outside all expected ranges, then the Ploidy Estimator does not determine a sex karyotype. 100% recall and precision were achieved across all chromosomes in 21 samples with various triploid and sex chromosome aneuploidies as well as 2 normal samples. Accuracy was assessed using PASS calls from the ploidy.vcf. For more see [DRAGEN documentation](/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/ploidy-calling/ploidy-estimator.md).

**Example: HG00142 trisomy event**

HG00142 is reported in Polaris whole chromosome events as an example with chromosome-level copy number gains consistent with trisomy.

<details>

<summary>HG00142 chromosome-level ploidy metrics (click to expand)</summary>

| CHROM | median | mad | z-score |
| ----- | ------ | --- | ------- |
| chr11 | 130.4  | 9.6 | 169.4   |
| chr13 | 129.6  | 9.7 | 144.9   |

</details>

![HG00142 whole chromosome trisomy example](https://raw.githubusercontent.com/Illumina/Polaris/master/cohorts/1000_genomes/plots/chromosome_level_events_trisomies_3_2.png)

Source: Polaris whole chromosome trisomy events, sample HG00142.


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