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Hi,
I am attempting to smooth a genome graph created by the pggb pipeline on 348 genomes (HPRC + 252 trios + hg38 + chm13v2) on a chromosome by chromosome run.
However, for most larger chromosomes…
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Hi again,
I'm having serious troubles processing the `PGGB` _**.vcf**_ files... At first the tool pointed out to haplotypes being un-phased; this is a problem I fixed collapsing the columns for eac…
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#146
Hi,
I wanted to check if ordering the core genome had been added? If not, is there a way to use any of the outputs to control how the gene alignments are ordered? I'm currently looks at di…
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Hi. Does Panaroo provide a means for adding genomes to an existing pangenome generated with Panaroo? How can one add genomes while maintaining the existing gene names?
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Is there a way to not take SNPs and small INDELs into account in the final graph ?
I am looking for a way to have a Pangenome graph with only structural variants and translocations.
Thanks!
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Hi John,
Hope all is well.
I'm trying to run genespace on two mimulus genomes, using tomato as an outgroup. However, during the pangenome step I am getting this error as it tries to pull the no…
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Hi there,
My aim is to get a genome inference for a human sample (HG005) to benchmark my graph in terms of SVs calling using `PanGenIe`. I assembled both with `minigraph-CACTUS` (for which I'm test…
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Hi,
I have run the pggb for each chromosome fasta of pangenome. Does the HPRC graph have any downstream use in vg pipeline?
I have several questions.
1. How to combine the each chromosome gf…
baozg updated
2 years ago
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I'm getting an error when running "odgi flip" using an .og subgraph file built from an HPRC PGGB-generated graph from [here](https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=pang…
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I'm trying to load the HPRC PGGB-generated GFAs from here: https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=pangenomes/freeze/freeze1/pggb/chroms/
I get this error message:
`…