Haplotype variant quality metrics

The following metrics are calculated for haplotype variants.

Zygosity

• Indicates whether the haplotype is present on one chromosome or both, based on the genotype reported in the VCF.

VCF Filter

• Displays the value of the FILTER field in the VCF.

• Reflects whether the haplotype variant passed DRAGEN quality thresholds or failed one or more checks (e.g., depth, allele balance, phasing constraints).

• The platform shows the FILTER flag exactly as provided by the caller.

• Requires DRAGEN 4.3+.

Min. Genotype Quality

• Shows the genotype confidence score assigned by the caller.

• Higher GQ values indicate greater confidence in the phased genotype behind the haplotype.