Currently, indel realignment uses a mismatch quality score based approach for generating alternate consensuses. It is desirable to also support Smith-Waterman for generating consensuses. We have a Smith-Waterman implementation, but it needs to be integrated into the realigner itself.
fnothaft
commented
10 years ago
Currently, indel realignment uses a mismatch quality score based approach for generating alternate consensuses. It is desirable to also support Smith-Waterman for generating consensuses. We have a Smith-Waterman implementation, but it needs to be integrated into the realigner itself.