Contamination Threshold 100x Fix #1074
Merged
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
Missed this on contamination upper filter - TDR metrics are for out of 1.00 , not 100. Nothing affected in the most recent WGS callset , from the looks of things
bpblanken
approved these changes
Apr 8, 2025
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Outdated suggestions cannot be applied.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.
Missed this on contamination upper filter - TDR metrics for contamination rate are for out of 1.00 , not 100 as in GATK. I'd noted this previously (in a Slack message in a sea of other Slack messages) but didn't make sure it was persisted enough outside of that. Nothing affected in the most recent WGS callset , from the looks of things. Highest noted contamination rate otherwise was 0.044 , and that was flagged for low coverage anyways