issues
search
populationgenomics
/
automated-interpretation-pipeline
Rare Disease variant prioritisation MVP
MIT License
5
stars
4
forks
source link
Seqr integration changes
#308
Closed
MattWellie
closed
11 months ago
MattWellie
commented
11 months ago
Fixes
AIP doesn't currently export a data file suitable for ingestion into Seqr
Related:
https://github.com/broadinstitute/seqr-private/issues/1254
Exclusive conversation for cool people:
https://centrepopgen.slack.com/archives/C05A9MG77RN/p1686874444939489
Proposed Changes
Adds a new helper script to digest the current output into a minimised representation. Not (yet) part of the core workflow.
Metadata index contains the plaintext description of all current categories
Includes labels per variant (placeholder for improved variant prioritisation)
Boolean per variant for if variant is pathogenic alone - used in state & seqr outputs
Variant IDs for compound-het(s) to link with
Tests updated to reflect new content
Removed
supported
boolean from the output
Checklist
[x] Related Issue created
[x] Tests covering new change
[x] Linting checks pass
Fixes
Proposed Changes
supported
boolean from the outputChecklist