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**1. What were you trying to do?**
I want to convert a gbz pangenome graph (created using cactus-pangenome) into xg format.
```
vg convert -x canidpg.gbz > canidpg.xg
```
**2. What did you wa…
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Hello,
This is similar to a previous issue ' Using ODGI to remove complex regions #427 ', in which I'm also following the tutorial to remove complex regions from the HPRC pangenome graph: https://odg…
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**1. What were you trying to do?**
I am trying to reproduce the steps described in `https://github.com/cgroza/personalized_genomes_gbio/issues/1`, however, after I built the vcf file, and use `…
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**1. I mapped long reads to the graph *gbz.gfa using graphAligner and got the gam file. I wanted to to SV calling and genotyping
I ran the below command
apptainer exec cactus.sif vg pack -t 64…
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Hi !
I used your pipeline ` pangenome-graph-from-assemblies` to construct a VCF file, but I noticed that some of the variants have an unusually high number of alleles. see belows:
`1 18300 .…
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Hi,
We have dozens of plant HiFi assemblies of inbreeding line, my previous test work on pggb for parameters tuning. I noticed the newest version of cactus including updates of pangenome pipeline.…
baozg updated
2 years ago
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Hello there, thanks for developing `odgi`
I want to make a query to my pangenome graph and I thought I could do it with `odgi`, but I have struggled to find a way of doing it.
The query should …
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Hi!
So far I’ve been mostly playing around and testing the tools from which raised two questions. Using `cactus-pangenome` I have built a graph of 15 reference potato genomes but with just a singl…
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I am working on a graph-based pan-genome construction for ten genomes from the same crop whose genome size is less than 500 Mb. When following the Minigraph-Cactus Pangenome Pipeline to construct the …
Sunhh updated
2 years ago
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Hi
I'm getting an error about tbi indexing during a cactus-graphmap-join run.
I run the following command:
```
cactus-graphmap-join /cactus/jobStore --indexCores 30 --vg ${original_folder}/*H/…