Merfin v1.1

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 (uses k*)
  • Reference is partially from the same individual, or copy-number estimates are unstable. This mode disables k*.
    • -better: Almost identical to -polish, with k* 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

merfin v1.0

The first official release of Merfin. To compile from source run make in the src folder.