BAM trimming according to primers with ivar, new rule #113
Conversation
This file contains 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
|
Dose iVar ork well? |
|
Related tool that we might want to integrate as well:
Background:
|
|
integrated as of git commit 5154bbb Currently in branch tribble, comming into branches and rubicon |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
The rule is rather simple, works in my internal snakemake on Euler
Fixed the problem I had with iVar, finding the -e switch, which outputs also reads that were not trimmed.
This is not too logical in iVar, compared to other trimming software I've used.
Added also in the same rule samtools sorting and indexing, copying your style from align.smk.
The pull request does not change anything in your files, just adds 3 files...