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Implement multiallelic variants/variant normalization #447

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holtgrewe opened this issue May 16, 2024 · 2 comments
Open

Implement multiallelic variants/variant normalization #447

holtgrewe opened this issue May 16, 2024 · 2 comments
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enhancement New feature or request

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@holtgrewe
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Is your feature request related to a problem? Please describe.
Currently, mehari does not support multi-allelic sites. This is a big limitation and requires bcftools norm -m -any --force.

Describe the solution you'd like
Allow mehari to process multi-allelic sites. Mehari will also need to normalize the sites for precise predictions for which it will need to be given the FASTA reference. When writing out the split/normalized records, mehari will need to sort the variants again so the resulting VCF file is sorted.

Describe alternatives you've considered
N/A

Additional context
N/A

@holtgrewe holtgrewe added the enhancement New feature or request label May 16, 2024
@tedil
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tedil commented May 21, 2024

But why should normalization functionality be replicated in mehari? Makes much more sense to stick to bcftools norm, since that already exists and is (in some way or another) tried and tested and there's no need to maintain even more functionality.
When encountering multi-allelic sites, simply bail and remind the user to normalize.

@holtgrewe
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VEP can handle it so should we...

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Labels
enhancement New feature or request
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