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Hi:
I'm looking at some 30x ONP human genome data and seeing that sniffles appears to overcall variants as translocations (BND) when in fact they contain a duplication. These BND variants are being f…
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This issue is part of an effort to reconcile the current [structural_variant database model](https://github.com/cBioPortal/cbioportal/blob/87e5a228d80a31515bf1a3e762bd2d70db89d2fb/db-scripts/src/main/…
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Annotation for balanced structural variants is messy at the moment; e.g. an inversion will show a lot of genes between the breakpoints with all kinds of functional annotations, like start_lost etc as …
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For some of my samples, purity estimation fails. In such cases, the copy number track from purple has a lot of noise, likely because it is being scaled up by (1/purity). I want to be able to use the c…
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Thank you for your excellent work!
I wonder if I run the haphic pipeline correctly. I have a genome of 4G (a diploid, 2n=26), and I just use the p_ctg.fa file from hifiasm and HiC data. When I run…
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Hello ,
I am trying to run structural variants annotations using annovar. Do annovar support it? If so can u help me with how to toggle structural variants input so the algorithm can get that?
R…
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I'm working to identify SVs in 10X linked-read data using methods alternative to longranger. What is the best way to call SVs from the adjacency info given in the bedpe file, or is there a tool that d…
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Hello!
I am building pangenome graphs for inversion regions in Atlantic herring. In the first case below (image 1a and 1b), I constructed 1b graph by reverse orienting all the sequences but keeping…
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When listing genes included in structural variants what is the order the genes are listed? would it be possible to keep the genomic order instead? this will be much more useful specifically to be able…
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Once #1824 goes in, we will have the option to support recursive functions. But, in order to do so, we will need to make changes to the IR and codegen.
Blocked by:
- [x] #1824
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The IR wou…