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Which annotation tool should be used for running DriverMl #13

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bagieutopia opened this issue Jan 13, 2025 · 0 comments
Open

Which annotation tool should be used for running DriverMl #13

bagieutopia opened this issue Jan 13, 2025 · 0 comments

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@bagieutopia
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I have run DriverML with my variant data which was previously annotated using Funcotator2 I manually changed the variant classification further to match the terms prescribed in your documentation (Silent, Missense_Mutation, Nonsense_Mutation, Splice_Site, Frame_Shift_Del, Frame_Shift_Ins, In_Frame_Del, and In_Frame_Ins). However, upon running except 1 all the variants in my file have a high P value and hence unusable. Can you please recommend fixes for this? which annotation tool do I use to avoid manually renaming the variant classification terms. Also my cohort doesn't have any normal samples so during variant calling I ran mutect2 on tumor only mode with hg38 as reference could this be the issue? please advice

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