Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Hotfix 1.5.x - fix MNV coordinates #197

Merged
merged 5 commits into from
Feb 25, 2021

Conversation

julie-sullivan
Copy link
Collaborator

The MNV positions were incorrect. Here's an example:

ClinVar ID: 266834
chr13:32316508:GAC:ATCGATCGAT

Decomposed variants

Dragen CellBase output
13:32316508:G:ATCGATCG 13:32316508::ATCGATC
13:32316510:C:T 13:32316517:C:T << wrong

The coordinates are calculated with the start, and the index:

genomic start + current index = start

Previously the code was using the index for the right aligned string, which was "-------GAC"

32316508 + 9 (index of -------GAC) = 32316517 << incorrect

I've updated the code to use the index of the original "GAC"

32316508 + 2 (index of GAC) = 32316510 << correct

@imedina imedina added the bug label Jan 22, 2021
@imedina imedina requested a review from j-coll January 22, 2021 19:59
@imedina imedina merged commit f0f3ee6 into opencb:hotfix-1.5.x Feb 25, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants