CountVariants
From GSA
CountVariants is an evaluation module for VariantEval. It computes the following metrics:
| Metric | Definition |
|---|---|
| nProcessedLoci | Number of processed loci |
| nCalledLoci | Number of called loci |
| nRefLoci | Number of reference loci |
| nVariantLoci | Number of variant loci |
| variantRate | Variants per loci rate |
| variantRatePerBp | Number of variants per base |
| nSNPs | Number of snp loci |
| nInsertions | Number of insertion |
| nDeletions | Number of deletions |
| nComplex | Number of complex loci |
| nNoCalls | Number of no calls loci |
| nHets | Number of het loci |
| nHomRef | Number of hom ref loci |
| nHomVar | Number of hom var loci |
| nSingletons | Number of singletons |
| heterozygosity | heterozygosity per locus rate |
| heterozygosityPerBp | heterozygosity per base pair |
| hetHomRatio | heterozygosity to homozygosity ratio |
| indelRate | indel rate (insertion count + deletion count) |
| indelRatePerBp | indel rate per base pair |
| deletionInsertionRatio | deletion to insertion ratio |
