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Genmod annotate chromosome names missmatch for mitochondrial variants #499

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fellen31 opened this issue Nov 12, 2024 · 0 comments
Open

Genmod annotate chromosome names missmatch for mitochondrial variants #499

fellen31 opened this issue Nov 12, 2024 · 0 comments
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Description of the bug

Genmod annotate uses ensembl names (MT) by default, and can't therefore annotate variants on chrM.

This could be solved by providing a custom gene list to genmod annotate, or perhaps by using the --vep keyword in later steps of genmod.

But also see: Clinical-Genomics/genmod#149

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@fellen31 fellen31 added the bug Something isn't working label Nov 12, 2024
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