11 Implementation Notes

Homozygous variant counting

Prior to evaluation, all homozygous variants with genotype 1|1 are split into two heterozygous variants 0|1 and 1|0 (with identical reference and alternate alleles). We do this because variants on separate haplotypes may be realigned to a new representation, and to deal with cases where only one of the two calls is correct (or part of a complex variant). Thus, a fully-correct homozygous variant call will be counted as two true positives, whereas most other evaluation tools will count one true positive.

Quality score sweeping

For precision/recall and alignment distance calculations, when sweeping quality scores, only the query variants are filtered.

Limitations

The current version of vcfdist is not designed to support:

• somatic variants
• unphased variants
• overlapping variants (on the same haplotype)
• polyploid contigs