Regarding data screening

[vinitamehlawat]

Hi @qianjiaqiang

Sorry for bothering you again; I ran the VENAS on my data, which included all omicron lineages (on default parameters, -b none, -r 0), but I realised that it was only giving me the backbone network of the BA.2 lineage, not all Omicron lineages. However, I ran VENAS seprately on only the BA.1 & BA.1.1 lineages and it gave me networks for both lineages. How VENAS selectively screens out these lineages in the first run while not eliminating the BA.1 and BA.1.1 lineages in the second run.

It would be quite helpful if you could assist me in resolving my problem

Thanks Vinita

[qianjiaqiang]

Maybe it depends on your data?

If BA.2 have more small mutation lineages than BA.1 ,BA.1 would be included in BA.2 lineage.

And if your network only includes omicron lineages , the BA.2 will be the most important cluster center of all the network.

When your network is not large enough, you can try adjust threshold in the file main_path.py:65 or use small mode(main_path_example.py:6 main_path.process(G,coms,mode="small")).

[qianjiaqiang]

Because VENAS is optimized for large network，so some parameters or the algorithm may not work very well on small network.