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Update vg rna to project reasonably onto haplotypes containing CNVs #4399

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jeizenga opened this issue Sep 13, 2024 · 0 comments
Open

Update vg rna to project reasonably onto haplotypes containing CNVs #4399

jeizenga opened this issue Sep 13, 2024 · 0 comments

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@jeizenga
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Pertains to #4397.

To do this, we need to be able to identify predecessor/successor on the output of locate queries from the GBWT to enforce colinearity constraints on the haplotype sequences through exons. @jltsiren tells me that this is possible with the R-index. However, this will require building the R-index alongside the GBWT in the vg rna pipeline, as well as its implementation in vg autoindex.

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