-
@glennhickey Is it possible to generate a pangenome graph with only SVs while retaining W lines? The pangenome graph generated by minigraph lacks W lines.
-
**1. What were you trying to do?**
I want to use vg surject to convert the GAM file into the BAM file format,so I need to use **convert** to generate the xg graph.
**2. What did you want to ha…
-
Hi Sam,
Thanks for developing ggCaller and it is wonderful. Recently, I used ggCaller v1.3.4 on my Ubuntu 22.04.3 LTS system to generate a pangenome graph for 73 bacterial genomes with the followin…
-
Hi @chg60 ,
Thanks for working on `phamsseqs`. I was wondering if it is possible to keep the [db.tsv cluster file](https://github.com/soedinglab/MMseqs2/wiki#cluster-tsv-format) from the `mmseqs` o…
-
# **This issue post is for prosperity and has already been reported.**
I have been using Panaroo for a while now but I am currently trying to take the DNA/Protein sequences reported in the combin…
-
I have a genome-wide GFA file and reference genome file and VCF file.
Pan-genome was constructed using Minigraph-Cactus.
In this pan-genome, the inserted fragment will contain some SNP and INDELs…
-
I am using vg 1.51.0 to try and call snp and indel (vg call -a) from simulated short-read data mapped to a pangenome using giraffe. The true set is obtained by downsampling from the variation set o…
-
For some reason we end up with 0 genic regions:
```
Number of Genic Regions: 52039
Number of genicRegions Before Merge: 0
```
The suspect code in question is [this Kotlin lambda](https://bitb…
-
Hi, I have the following questions to ask:
1. How to add new samples and contigs to an existing pan-genome, and whether it can be done directly using the _minigraph_ tool.
2. How to merge pan-genome…
-
Hi thank you for your nice tool.
I've encountered problem while using ggcaller v1.3.4. (error log is below the description part )
I created conda environment and installed ggcaller following offic…