8000 Write functions for genomic liftover GRCh37->38 · Issue #147 · biocommons/anyvar · GitHub
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Write functions for genomic liftover GRCh37->38 #147

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ahwagner opened this issue May 2, 2025 · 2 comments
Open

Write functions for genomic liftover GRCh37->38 #147

ahwagner opened this issue May 2, 2025 · 2 comments
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enhancement New feature or request

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@ahwagner
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ahwagner commented May 2, 2025

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

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Potential Impact

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Additional context

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None

@ahwagner ahwagner added the enhancement New feature or request label May 2, 2025
@theferrit32
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Idea is to add this functionality in an http middleware handler to automatically do it for every new variant

async def add_creation_timestamp_annotation(request: Request, call_next) -> Response:

@theferrit32
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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

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