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Generating a Clipped/Filtered Graph from a {graph_name}.full.gbz File produced by the MC pipeline? #4452

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EEEdyeah opened this issue Nov 23, 2024 · 0 comments

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@EEEdyeah
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Hello,

I have {graph_name}.full.gbz files generated from Cactus Minigraph to map short-read data. According to the tutorial, a filtered graph is more efficient for vg giraffe. Additionally, I noticed that Haplotype Sampling is a better option for vg giraffe, requiring a clipped .gbz graph and a .hapl file.

How can I generate the filtered/clipped version of the graph and haplotypes without having access to the original input files?

I tried the following steps but am not sure if they are correct: (I only have full.hal full.gbz. full.gfa files)
vg convert -g <(gunzip -c {graph_name}.full.gfa.gz) > {graph_name}.full.vg
cactus-graphmap-join --vg {graph_name}.full.vg --hal {graph_name}.full.hal --giraffe clip ...

Any suggestions or corrections to this approach would be greatly appreciated. :)

@EEEdyeah EEEdyeah changed the title How to manually generate a Clipped/Filtered Graph from a {graph_name}.full.gbz File produced by the MC pipeline? Generating a Clipped/Filtered Graph from a {graph_name}.full.gbz File produced by the MC pipeline? Nov 23, 2024
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