SNV, MNV, and indel quality metrics

The following metrics are calculated for SNVs, MNVs, and indels.

The MNV variant type is supported from version 100.39.0.

VCF Filter

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

• Requires DRAGEN 4.3+.

Base Quality (BQ)

• Average Phred score for bases supporting the variant.

• High BQ indicates more reliable base calling.

Depth (DP)

• Total number of reads covering the position.

• It is the count of aligned reads after the removal of duplicate reads and/or reads with MQ=0.

Mapping Quality (MQ)

• Confidence in read placement on the reference genome (Phred-scaled).

Genotype Quality (GQ)

• Confidence in the zygosity call.

• It is derived from likelihood ratios between genotypes and scaled as Phred.

• This metric is not relevant for mtDNA variants.

Phasing

• Numeric phase block identifier for TruPath Genome data.

• If a phased genotype is available, the platform appends _A for genotype 1|0, _B for genotype 0|1, or _AB for genotype 1|1.

• Requires DRAGEN 4.5+ and version 100.40.0+.