Handle records with empty EVIDENCE field in MakeCohortVcf #233
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
mwalker174
reviewed
Sep 17, 2021
| @@ -47,6 +47,8 @@ The following are the main pipeline outputs. For more information on the outputs | |||
|
|
|||
| ### Pipeline overview | |||
|
|
|||
| <img alt="pipeline_diagram" title="Pipeline diagram" src="https://i.imgur.com/ZTBjo1i.jpg" width="1000"> | |||
There was a problem hiding this comment.
It would be better to host this in the repo, can you put it in the root dir?
mwalker174
approved these changes
Sep 17, 2021
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Outdated suggestions cannot be applied.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.
Updates
Add handling for records with empty EVIDENCE fields in overlap_breakpoint_filter.py in MakeCohortVcf.ResolveComplexVariants.BreakpointOverlap. Records have empty EVIDENCE fields if they are all-ref but "salvaged."
Unrelatedly, also added pipeline diagram to Terra dashboard. Live on 1kgp workspace.
Testing
Tested with 1kgp batches on Terra with updated docker image - successfully ran where it had previously failed on chrY.