Hi, Can `vg deconstruct` or any other vg/minigraph-cactus tool export a GATK-style all-sites gVCF from a pangenome graph? I understand that `vg deconstruct` creates VCF …

Hi everyone, I'm having trouble building the distance index (.dist) for a large plant pangenome graph generated by Minigraph-Cactus, and would appreciate any advice. I'm …

Hello, I've found strange behavior surrounding the vg's gbwt index and wanted to report it and potentially figure out why it occurs. When I create …

Hi everyone, I am aiming to identify and genotype structural variants in a cattle cohort by mapping short reads against a [Minigraph-Cactus][3] pangenome graph. To …

I'm using `vg giraffe` to align short-read sequencing data to a minigraph-cactus pangenome graph. When I checked some repetitive regions, I noticed that reads that …

Hi everyone, in the [minigraph-cactus pangenome pipeline][1], normally several fasta files are used. However, I am curious, is there any way to utilize cactus to …

Dear vg team, Thank you for the great program. I encountered an issue while testing the minigraph GFA file using HPRC in the vg deconstruct …

I'm trying to generate a GAF (with reference rather than node coordinates) which describes how an individual long-read maps to all the different components of …

I did a small comparison of total mapping of a small short-read dataset to: 1. a graph constructed using cactus-minigraph composed of eight whole genome …

Hi! I'm using `vg rna` for transcriptomic analyses following the [wiki](https://github.com/vgteam/vg/wiki/Transcriptomic-analyses). I will list each of my steps and confusion below： - First, I started …