Add pairtools min_mapq option and release 0.2.1#9
Merged
Conversation
Release 0.2.0: fix Hi-C QC report rendering and pipeline improvements
Expose pairtools min_mapq in config.yaml and schema.yaml, pass --min-mapq to pairtools parse so multi-mapped reads (BWA MAPQ 0) can be kept in the contact map. Switch bwa_split options to -5SP and raise pairtools memory to 8G.
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
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Summary
min_mapqinconfig.yamlandschema.yaml, and pass--min-mapqtopairtools parse. Set to 0 to keep multi-mapped reads (BWA assigns MAPQ 0 to multimappers) in the Hi-C contact map. Defaults to 1 (pairtools default).bwa_splitoptions to-5SP(Hi-C-appropriate; drops-M).Test plan
min_mapqint field.pairtools parseinvoked with--min-mapq {params.min_mapq}.