feat: normalize candidate calls in case of multiple samples in a calling group #99
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
johanneskoester
changed the title
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Outdated suggestions cannot be applied.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.
Normalize whenever we call more than one sample per group
The reason is that in complex scenarios, we want primitive alleles
in order to be able to correctly identify events.
Example:
The child has
CGAGCGGA -> TGGCTGGA
while both parent have
CGAGCGGA -> TGGCTGGG
The correct genomic interpretation is that the G allele in the end is lost in the child.
But in above MNV representation, it looks like a denovo event overall, while the two SNVs at the beginning are actually inherited.
cc @christopher-schroeder