Tag: PGGB

Lack of correspondance of GFA node IDs to giraffe/call node IDs

I have a GFA graph built with PGGB using several samples. I want to genotype some other samples with short reads using VG Giraffe. After investigating how to generate the corresponding indexes for VG Giraffe from a GFA generated with PGGB, I think I have found a way to do…

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Challenges in Variant Calling and Genotyping with Short-Read Data Mapped to a Pangenome Graph: Seeking Guidance

Challenges in Variant Calling and Genotyping with Short-Read Data Mapped to a Pangenome Graph: Seeking Guidance 0 Hello all, We are reaching out since we have some practical questions regarding variant calling and analyses of short-read data mapped to a pangenome graph. We are working on a project aimed to…

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Interpretation question regarding vg call result vcf

Thank you so much for creating such an amazing tool. I am currently having difficulty interpreting vcf results from vg call. I currently performed haplotype-resolved genome assembly and created a graph-genome using both haplotypes (HA and HB) via pggb and vg. Afterwards, a variant called vcf was completed through vg…

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Analysing short reads mapped to a pangenome graph

Analysing short reads mapped to a pangenome graph 0 Hello all, Research that I am working on requires me to identify organisms and specific genetic information that these organisms carry. The way I do this, is by first constructing a pangenome graph of several other organisms, to capture most of…

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Construct a pantranscriptome reference with two haplotypes from a single sample.

Construct a pantranscriptome reference with two haplotypes from a single sample. 0 Hello, I am trying to construct a graph reference for rpvg using two haplotypes from a single sample. I created a GFA file from two haplotype from single sample with pggb. Then, I generated VCF file and graph.pg…

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Open problems in genomics 2023

As a user and developer I am grateful for all the efficient, clever and really helpful tools and pipelines put out there by the community. I’d like to use this page to suggest any open questions from my point of view, i.e gaps in the field where talented developers might…

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Explanation of vg deconstruct vcf output

Explanation of vg deconstruct vcf output 0 Hello, I am struggling in understanding the vg deconstruct vcf output. I’m working on a pangenome (17 genomes, reference included) and the file has been created thanks to the pggb pipeline. Is there a detailed explanation of the vcf decomposed file anywhere? Especially…

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Creating a variation graph for Giraffe alignment from assemblies

Creating a variation graph for Giraffe alignment from assemblies 0 I have a collection of ~100 4.5 megabase haploid assemblies that I would like to map to using giraffe. However, I am not completely clear on what the best practices are to construct the graph starting from the assemblies. I…

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