SACGF / SACGF/variantgrid

Consider showing >50 base variants as symbolic (when we can)

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#1,008 1 comment 0 reactions 0 assignees View on GitHub
enhancement
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Python
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9h 28m
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Description

Currently, we represent Structural Variants (SVs) as symbolic alts (```, , ```) when they are above 1000 bases

But, 200 bases or even 50 is starting to get unwieldy - eg in variant search results, or variant coordinate in a classification

The reason we used 1000 bases is because long SVs crash the annotation pipeline, so we have a special "CNV" pipeline that has a few options turned off. Using explicit ref/alt means that we get a slightly better annotation, at the expense of speed (and possibly crashes, though we have found sub 1000 bases is fine)

You can convert between these formats without loss, so there is no reason why we couldn't store say 200bp length variants as explicit in the DB but as symbolic to the user

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