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The vg version I use: version :
v1.59.0
I used PGGB to construct a pan-genome (GFA); I want to rely on him to find the SNP of the sample; Here's my current script:
vg autoindex -t …
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I'm trying to train your model on the VG Dataset to reproduce the results. But I could not find the source for these files : VG-SGG-train.h5、VG-SGG-test.h5、VG-SGG-val.h5 in [lavis/configs/datasets/vg/…
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I couldn't find the file VG-SGG-train_zs_pred.h5/VG-SGG-train.h5 in the download link .Is this file the same as 'VG-SGG-with-attri.h5'? Or is VG-SGG-train_zs_pred.h5/VG-SGG-train.h5 a dataset file tha…
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I am trying to convert a HAL file from progressive cactus into a vg graph for structural variant calling using vg. Here are the steps I have used
```
hal2vg --refGenomes PWN --noAncestors --h…
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**1. What were you trying to do?**
Dear VG team,
After generating GFA files for each chromosome using PGGB, I need to merge them for Panacus. However, the Panacus team confirmed that a simple ca…
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Hey guys, thanks for the software.
I was following the tutorial for mapping long reads and calling SV.
All good for the first part, but I noticed that when I was launching the vg pack using the .gbz…
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Hi,
When trying to use the collection/role infra.lvm_snapshots.snapshot_create, it fails when there is lvm thin pool in the managed node. Snashot and rollback works fine with regular LVM but not wh…
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Hi, vg is a great software in pangenome.
I have 12 genome and gff files, and already built a graph-based pangenome with SV vcf file by _vg construct_ and _vg index_.
I also have some RNA-seq dat…
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I check out the result(GAM file) of vg map. I found that there are some question in base repeat region. If there is a few bp deletion/insertion, the mapping information may represent this mismatch in …
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Thank you for your great work! I was exploring the code and encountered some errors when I tried to evaluate the provided stage2 model (vg_stage2_predcls). I seems that I would need some files under f…