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Dear Sir, I compared the d2 index obtained by default from minigraph cactus with the d2 index I built using vg, but my graph pangenome results seem incorrect.
```
vg clip 97samples.vg -d 2 -P 035_C…
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I have test a small set of 10 fungi genomes (around 40M) according to the pangenome pipeline (https://github.com/glennhickey/pg-stuff/blob/main/cactus-pangenome.sh)
The steps were as follow:
I used …
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**1. What were you trying to do?**
Use vg deconstruct a gfa file into vcf file
**2. What did you want to happen?**
get a list a vcf file
**3. What actually happened?**
libgomp:
libgomp:…
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Hello rpvg team
I have a general question and I would appreciate your help.
I am trying to infer the haplotype expression of human-experiment reads using rpvg.
I have performed the construction o…
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Hello,
I'm trying to apply `bcftools consensus` using a cactus VCF file, but coming across overlapping variants in the process. I can see that the overlapping variants correspond to several level-1 v…
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The gene alignment step can take a long time to complete. Is it possible to add functionality to output the unaligned gene sequences to later align batches of them across a computing cluster? The pira…
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relevant to #309
I've been working on annotating catlases. In this use case, I built a "metapangenome" graph. I did a genome query (_R. gnavus_) in 605 gut microbiome metagenomes, and then combined…
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Hi,
I have been using FSA to align about 20 de-novo-assembled genomes that are about 1MB long. They are from different individuals in the same species. FSA runs, but it takes tons of memory, and …
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**1. What were you trying to do?**
calling structural variation after mapping long-read data on whole genome pangenome graph
**2. What did you want to happen?**
create a VCF file which contai…
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**1. What were you trying to do?**
I want to build GCSA index for a VG file generated from the Minigraph-Cactus Pangenome Pipeline. Because I met a "Size limit exceeded" problem in "vg index" run…
Sunhh updated
2 years ago