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Does indel effect the methylation calling or C context determination #145

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huichanghuang opened this issue Jun 14, 2023 · 1 comment
Open

Does indel effect the methylation calling or C context determination #145

huichanghuang opened this issue Jun 14, 2023 · 1 comment

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@huichanghuang
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huichanghuang commented Jun 14, 2023 •
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Hi, Since mapping bam file from bwa-meth does not include an XMtag like Bismark， Is there any way can I know how hpl indel effect the methylation call or C context determination?
Thanks.
Best regards,
Huichang Huang
@huichanghuang huichanghuang changed the title Does indel impact the methylation calling or C context defining Does indel effect the methylation calling or C context determination Jun 14, 2023
@dpryan79
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InDels themselves will be outside of the calls as well as the context, which is taken from the reference sequence.

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@dpryan79 @huichanghuang