STR quality metrics

The following metrics are calculated for STR variants.

VCF Filter

• The FILTER value in the VCF, indicating whether a variant passed caller thresholds or failed specific checks.

• Requires DRAGEN 4.3+.

Depth

• Coverage at the repeat locus.

Repeat Number

• Count of repeat units.

Repeat Length

• Base-pair length of the repeat tract.

Confidence Intervals

• Confidence intervals for the REF and ALT alleles, showing repeat-size accuracy.

• Requires DRAGEN 4.3+.

STR loci in the ARX and HOXA13 genes are always marked Low quality.