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Going from g. representations on GRCh37, we should be able to liftover to GRCh38 where applicable.
Add configurable functionality to enable automatic translation of the queried variant to other supported genomic context(s) and cache the relationship between these contexts for later retrieval.
Use case
For us to match across evidence and searched contexts in AnyVar queries, we will need to be able to transform across these two commonly used reference assemblies.
Acceptance Criteria
We can forward transform variants from GRCh37 to GRCh38, and vice versa.
NOTE: return with specific example inputs and outputs
Instead of creating a mapping table for the 37<->38 relationship, we will use the annotations table to store for each of them an annotation that says "liftover_to" / "liftover_of" the other VRS ID
Feature description
Going from g. representations on GRCh37, we should be able to liftover to GRCh38 where applicable.
Add configurable functionality to enable automatic translation of the queried variant to other supported genomic context(s) and cache the relationship between these contexts for later retrieval.
Use case
For us to match across evidence and searched contexts in AnyVar queries, we will need to be able to transform across these two commonly used reference assemblies.
Acceptance Criteria
We can forward transform variants from GRCh37 to GRCh38, and vice versa.
NOTE: return with specific example inputs and outputs
Proposed solution
Use AGCT (Another Genomic Conversion Tool).
https://github.com/GenomicMedLab/agct
Alternatives considered
No response
Implementation details
No response
Potential Impact
No response
Additional context
No response
Contribution
None
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