Can VG simulate the third-generations long reads? about vg HOT 5 OPEN

Although vg sim can run with long read input, it's really designed for short reads. If you use it to generate long reads, you won't get very realistic errors or a realistic read length distribution. In our own testing and development, we've used pbsim to simulate long reads. You would probably want to generate the reads from FASTAs of sample haplotypes, rather than directly from the GBZ file.

from vg.

Thank you!
And can I use vg sim and the .gbz file to generate short reads using vg sim -x graph.xg **-g graph.gbz** -m SAMPLE -n 1000 -l 150 -a > SAMPLE.gam ?
Now I have the .gbz file of all chromosomes pangenome graph. And I want to generate short reads only for chr21. Do I need to withdraw the .gbz file of chr21? I don't find Related command.

from vg.

Although vg sim can run with long read input, it's really designed for short reads. If you use it to generate long reads, you won't get very realistic errors or a realistic read length distribution. In our own testing and development, we've used pbsim to simulate long reads. You would probably want to generate the reads from FASTAs of sample haplotypes, rather than directly from the GBZ file.

I'm simulating long reads using pbsim3 and the output is .maf file. If I want to do some simulation experiment such as calling SV based on the simulation reads, can I use the maf file as the truth set? Or use some public truth set？

Do you have any suggestions？

from vg.

Looking through our script, it seems that we used the maf2sam subcommand of bioconvert.

from vg.

@tanger-code If you want to simulate from just one named path in the graph, you can use the -P option to vg sim.

But that simulates from just that path; it won't include variants in the graph that leave the embedded path.

I don't think we have a way to simulate from the connected component of the graph that contains a path, other than using vg chunk --components -p name-of-path to pull out that subgraph and then simulating from it.

from vg.