SV quality metrics

The following metrics are calculated for structural variants.

Structural variant callers use breakpoint clusters, depth shifts, and split-read evidence to compute quality. Large structural variants can fail quality thresholds even when the underlying biology is real.

VCF Filter (DRAGEN 4.3+)

• The FILTER column value in VCF indicating whether a variant passed the caller's quality thresholds or failed some checks.

Quality

• Represents the variant quality score as provided in the VCF.

Size

• Indicates the length of the structural variant.

Bin Count

• Represents the number of bins supporting the structural variant call.

CIPOS

• Start breakpoint confidence interval

• Extracted from VCF INFO: CIPOS and displayed as two integers [lower, upper]. The interval width (upper - lower) determines the confidence level of the start breakpoint:

  • High (0–20)

  • Moderate (21–100)

  • Low (>100)

• Available from v100.40.0+ versions.

CIEND

• End breakpoint confidence interval

• Extracted from VCF INFO: CIEND and displayed as two integers [lower, upper]. The interval width (upper - lower) determines the confidence level of the end breakpoint:

  • High (0–20)

  • Moderate (21–100)

  • Low (>100)

• Available from v100.40.0+ versions.

Paired Read Support (PR)

• Extracted from VCF FORMAT: PR.

  • PR[0] indicates number of paired reads supporting the reference allele (REF)

  • PR[1] indicates number of paired reads supporting the alternate (ALT) structural variant allele.

• Available from v100.40.0+ versions.

Split Read Support (SR)

• Extracted from VCF FORMAT: SR.

  • SR[0] indicates number of split reads supporting the reference allele (REF)

  • SR[1] indicates number of split reads supporting the alternate (ALT) allele.

• Available from v100.40.0+ versions.