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Hi
I'm using fastEPRR v2.0 and I'm getting a consistent error when reaching step 2 after I have ran step 1 on each chromosome.
I've been getting this error:
```
srun -n 1 singularity exec --…
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Interest have been expressed about visualizing graphs from pggb into Panache ( cf nf-core/pangenome#197), but the steps to convert formats are currently unclear.
Some documentation highlighting how…
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**1. What were you trying to do?**
Call variants from read support.
**2. What did you want to happen?**
Generate a VCF file.
**3. What actually happened?**
The command have been running…
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Determine the requirements and potential options for the basis of the Pangenome Annotation RNA-seq pipeline.
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Hello, authors,
At the demo, 'test-variants.vcf' was a regular variation vcf file. I am confused which step used the graph pangenome format with Extended Data Fig. 1. I used the 'pangenome-graph-…
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Hi,
A recent paper, "Comparing methods for constructing and representing human pangenome graphs", shows that pggb cannot construct graphs from 104 human haplotypes because of low computational eff…
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**1. What were you trying to do?**
I was trying to performe the augmentation step before variant calling to call variants from a set of illumina WGS reads that I've aligned to my vg graph. I'm runn…
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Just an issue to collect any relevant papers. For example, there's a whole Genome Biology issue on graph genomes at
https://www.biomedcentral.com/collections/graphgenomes (also see "Pangenome Graph…
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At 70 genomes and 109GB of graph data
```
-rwxr----- 1 kevin kevin 109G Jun 26 08:10 pangenome.lemongraph
-rwxr----- 1 kevin kevin 8.0K Jun 26 08:42 pangenome.lemongraph-lock
```
Not sure why, …
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I created a pangenome graph using pggb, resulting in gfa and og files. I now wish to perform some mappings to the graph and have a few questions:
1. From the pggb documentation I understand that the …