feat: fusion calling #222
Merged
feat: fusion calling #222
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
…eq-varlociraptor into fusion_calling
|
To get this running we need suhrig/arriba#191 being merged and a new release of arriba. |
FelixMoelder
commented
Sep 7, 2023
…to fusion_calling
johanneskoester
requested changes
Feb 19, 2024
| @@ -0,0 +1,90 @@ | |||
| #!/bin/bash | |||
There was a problem hiding this comment.
Does this script come from arriba sources? Please cite the full URL here.
There was a problem hiding this comment.
And is the license compatible?
There was a problem hiding this comment.
The license of arriba is also MIT and therefore compatible. :)
johanneskoester
requested changes
Feb 26, 2024
johanneskoester
approved these changes
Feb 26, 2024
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Outdated suggestions cannot be applied.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.
These changes introduce fusion calling in addition the variant calling.
There for arriba is applied for calling variants. As vep does not provide any helpful information it is skipped for fusion calls.
Instead annotation is performed by additional scripts that come with the arriba package.
To define a what kind of analysis shall be performed for a sample an additional column named
datatypehas been added to the samplesheet allowing eitherrnaordna. As file name extensions within the pipeline are separated intovariantsandfusionswe probably should unify this as the former one might also be too generic.For fusion calls a separte datavzrd report will be created adding a new category showing up in the final snakemake report.