Table 1 Format of the evaluation data
From: VPMBench: a test bench for variant prioritization methods
Attribute | Name | Description | Values |
|---|---|---|---|
Unique Identifier | UID | The unique numerical identifier of the variant | \({\mathbb {N}}^{\ge 0}\) |
Reference Genome | RG | The reference genome used to call the variant | String |
Chromosome | CHROM | The chromosome in which the variant is found | \(\{1,\dots ,22,\text {X},\text {Y},\text {M}\}\) |
Position | POS | The 1-based position of the variant within the chromosome | \({\mathbb {N}}^{\ge 1}\) |
Reference | REF | The reference bases | \(\{\text {A},\text {C},\text {G},\text {T}\}^*\) |
Alternative | ALT | The alternative bases | \(\{\text {A},\text {C},\text {G},\text {T}\}^*\) |
Variation type | TYPE | The variation type of the variant | \(\{\text {SNP},\text {INDEL}\}\) |
Classification | CLASS | The expected classification of the variant | \(\{\text {benign}, \text {pathogeneic}\}\) |