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**1. What were you trying to do?**
I wanted to perform augmentation using gam file mapped through vg giraffe on my pangenome graph.
**2. What did you want to happen?**
Successfully augmented grap…
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Hello,
As an experiment, I've tried take the vcf of the draft human pangenome, use bcftools +setGT to unphase the pangenome vcf, and then rephase the vcf using different reference panels. I am usin…
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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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Hi, I ran cactus-pangenome pipeline with `--binariesMode local` on server, the pipeline exited because of `bgzip` error.
> [2023-07-01T02:40:58+0800] [MainThread] [I] [toil.leader] Finished toil ru…
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My code is as follows:
cactus-pangenome ./js grch38_pan.seqfile --reference GRCh38 --outDir ./grch38_pan --outName grch38_pan --gbz --giraffe --vcf --chrom-vg --refContigs $(for i in `seq 22`; do pr…
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Hello,
I find there are a fewer SNP overlap rate between the callset form pangenome-graph-from-assemblies and the GATK results. What could be the reason? The article seems to only compare the abili…
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Hi,
I'm running minigraph-cactus v2.8.1 for a small region of a genome with the following command:
```
singularity exec --contain --bind $(pwd):/data $SCRIPTS cactus-pangenome \
/data/jobstore $fa…
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Hi,
We have dozens of plant HiFi assemblies of inbreeding line, my previous test work on pggb for parameters tuning. I noticed the newest version of cactus including updates of pangenome pipeline.…
baozg updated
2 years ago
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Hi all,
I'm running the Pangenome Pipeline using the latest Cactus binary realease (cactus-bin-v1.3.0.tar.gz). The first two steps went well, while the last one, cactus-align, returned me an error …
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At least:
- pangenome from only de-novo assemblies (should be of higher quality)
- pangenome from de-novo assemblies and read mapping experiments (reference biased)