Generating a Clipped/Filtered Graph from a {graph_name}.full.gbz file

[EEEdyeah]

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. :)

[zhangyixing3]

Hi, I think it will help you a litter #1469. I generated filtered graph from clipped graph and I wanted to perform vg giraffe with different filtered graph.

[EEEdyeah]

@zhangyixing3 Thanks! I was wondering, why do you use [vg clip] multiple times instead of putting all the parameters into a single command? Also, I noticed the first vg clip used -d 2, while the second one used -d 1. What would happen if I wanted to use -d 10 instead?