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Convert SMN1 SMN2 variants to SV VCF call format #241

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Jakob37 opened this issue Oct 17, 2024 · 0 comments
Open

Convert SMN1 SMN2 variants to SV VCF call format #241

Jakob37 opened this issue Oct 17, 2024 · 0 comments
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@Jakob37
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Jakob37 commented Oct 17, 2024

Currently these are presented in SMA CN tab in Scout.

If we could get them into SV VCF format, then the geneticists could work with these variants using existing tools.

This might concretely mean implementing a script doing the conversion and adding that into the ol' wgs downstream of the SMN[12] copy number caller step.

We would also need to check / coordinate with the geneticists whether all needed info then is presented in Scout.

@alkc alkc self-assigned this Oct 17, 2024
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