Fix coverage calculation to reduce false positives #22
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
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Outdated suggestions cannot be applied.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.
The current coverage calculation is using the total genome length to calculate the mean chromosome coverage. Instead the chromosome length should be used. This is also calculated on line 47 but for whatever reason overwritten by the total genome length value which is removed in this PR.
The error means that for each chromosome the coverage has been calculated too low. Furthermore since the coverage is used to calculate the threshold for calling candidates as "PASS" or "FAIL", this threshold has been calculate too low. This would in turn lead to the higher false positive rates if relying on "PASS" entries.
Note that this PR should follow #20.