Polishing modes added that does not use k* (reference is partially from the same individual as the reads, or reference vs. read copy numbers are not expected to match).
- filter variant calls for polishing
- Reference is from the same individual:
-polish(usesk*) - Reference is partially from the same individual, or copy-number estimates are unstable. This mode disables
k*.-better: Almost identical to-polish, withk*disabled (deprecated)-loose: Remove variants only when the num. missing (error) k-mers increase. Neutral alternate paths that score equally to the reference path are included.-strict: Include variants only when the num. missing (error) k-mers decrease. Neutral alternative paths that score equally to the reference path are excluded
- Reference is from the same individual: