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Hello
I have run the test data of cactus-minigraph, but the VCF file only have the sample for each haplotype, without the variation information. Please help me. Is this the correct result?
Below…
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Walk/W-lines are used to keep sequence walks through the graph. There are a few options:
1. Don't add W-lines as we already have Path/P-lines in GFA1. However, there are multiple problems with P-li…
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Dear SuperPang,
We are working on a plant genome to create a core chromosome set. To begin, we selected one chromosome from three different assemblies and trimmed the initial sequences (using head -n…
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Thank you for developing such a great program! I've been using ppanggolin msa and it's been helpful. Here is the command I've been working with:
ppanggolin msa -p Pangenome_graph/pangenome.h5 --p…
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The annotation approach added in #282 seems to be working out pretty well, and I had a few thoughts about how to extend and/or regularize it, as well as how to evaluate it.
My major realization is …
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Hi, @mnshgl0110
I am using wfmash alignment to do variant calling from the assmebly. Although `SyRI` support the PAF file since the version 1.6, but the native PAF from `wfmash` produce very diffe…
baozg updated
2 years ago
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Hello,
especially with the advent of phasing, I find myself needing more and more gfa instead of fasta, or in complement. I wonder if there is a tool in samtools to convert a sam to gfa? If not, I…
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**1. What were you trying to do?**
I was attempting to convert a pggb pangenome graph to gbz format for use in Giraffe.
**2. What did you want to happen?**
I wanted a direct conversion …
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Hi, “Summing up, we called odgi heaps -i -S -n200 to generate pangenome saturation curves for 200 permutations. ” From the article “A draft human pangenome reference”。
But when I try to run with my …
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Hello,
I am running the HPRC pangenome pipeline step by step for the first time and managed to run all the initial 4 steps successfully. However I am getting a "vg: invalid option -- 'S'" error in …