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### Description of feature
The pipeline should also be able to predict putative Neo-epitopes based on structural variants (SV). Currently we only support SNVs and small indels. Predicting Neo-epitope…
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### Description of the bug
I am trying to run the pipeline on the HPC PDC-Dardel and get error messages that I am not able to make sense of. I post it here in case you have any tips on how to figure …
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Hi,
I split the 1000GP chrX VCF into nonPAR, PAR1, and PAR2 regions then tried creating .msav files with these but I encountered some issues. Below is the code I used.
```bash
#/usr/bin/env bas…
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Edit: despite the title this link list now contains all kinds of reference material for benchmarking/normal-filtering SV (including CNV) calls on a population level as well on single sample (mostly ce…
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I as wondering if AsmVar does "joint genotyping" of multiple samples, analogous to what GATK does for SNPs?
Does AsmVar do break-point resolution? For example, if I have a population samples with s…
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@jmonlong says we use `vg add` for some structural variant graph stuff.
Looking at the code, `vg add` does not appear to create paths for the alleles of the variants it adds.
This means we can't…
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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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## Plays
Possible questions for stylometry:
1) Role of Actor-Managers in altering plays:
This needs just performed versions
Maybe: List of Macready-only variants (based on difference from variant…
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Hello
I need some suggestions in simulating complex structural variants in Hifi reads file from PacBio
https://downloads.pacbcloud.com/public/dataset/HG002-CpG-methylation-202202/m64011_190830_22…