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**1. What were you trying to do?**
Understand the output VCF of ```vg call```
**2. What did you want to happen?**
Analyse VCF file, first retrieve which kind of variant is present in each po…
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I'm very sorry to bother you.
Recently, I choosed alt contigs on a chromosome to construct a pangenome which is similar to construct GRCh38 Alts Graph.
When I used a gbz file , gencode. v38. pri…
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### Description of feature
Hi,
I found [jbrowse pangenome visualization](https://github.com/pangenome/jbrowse-visualization) plugins. The good new is it requires the graph created by `pggb`. Additio…
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Hi @maickrau
Since the new release and as you mentioned in https://github.com/maickrau/GraphAligner/issues/28, per default `--precise-clipping` is turned on.
For my evaluation of reconstruction acc…
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For some reason there was an IndexError when running the method below, but since the variable `codon_alignment` was never initialized there was a UnboundLocalError raised as well claiming: _local vari…
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Hello,
I was curious to know how annotation is handled after 2 dbg graphs are merged using VariMerge? Is there an annotation tool (for bacteria) that the authors of this software would recommend al…
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Hello!
I am building pangenome graphs for inversion regions in Atlantic herring. In the first case below (image 1a and 1b), I constructed 1b graph by reverse orienting all the sequences but keeping…
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- [x] `public_sequence_resource` should be a link instead, https://github.com/arvados/bh20-seq-resource/graphs/contributors
- [x] **Big Prominent link** Online Demo Link to https://graph-genome.githu…
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Hi
I'm using vg tools v1.50.1 "Monopoli"
I've produced a graph from 7 different genomes of the same species using minigraph-cactus.
I've used the indexes produced from minigraph-cactus with `…
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I try to convert the xg from vg version 1.24 to maf using Maffer. However, the maffter reported that the xg version is too new to ba accepted. Is it possible to update the maffer?
input: vg index…