Update bwape.c #29
Open
Update bwape.c #29
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Addition of clipping score parameter, so users who are doing alignment with samples that may have legitimately unmapped mates (where the quality of the reference is known to be poor or possibly incomplete). You can disable SW of course, or you can just discourage clipping which we've found to be the the primary error mode for the SW step. Currently, bwa can generate some pretty strange clipped alignments, with only 22 base pairs matching out of, say, 100. This option can be used to tune that behavior.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Addition of clipping score parameter, so users who are doing alignment with samples that may have legitimately unmapped mates (where the quality of the reference is known to be poor or possibly incomplete). You can disable SW of course, or you can just discourage clipping which we've found to be the the primary error mode for the SW step. Currently, bwa can generate some pretty strange clipped alignments, with only 22 base pairs matching out of, say, 100. This option can be used to tune that behavior.