08 Alignment Distance

Alignment distance is no longer calculated during vcfdist's default evaluation, but can be re-enabled using the --distance flag. Instead of counting different categorizations of variant calls (SNPs, INDELs, SVs) which are ill-defined when complex variants are involved, this approach uses a purely sequence-based evaluation approach that is independent of variant representations. For this reason, it can be a useful supplemental comparison method.

vcfdist performs Smith Waterman alignment at Point B, or m=0, x=3, o=2, e=1. The total number of substitutions, insertions, and deletions parsed from this alignment are reported, as well as the total alignment score.

Please note that as vcfdist performs a sweep of variant quality scores, only query variants are filtered by the quality threshold.