question about confidence interval for INDELs

[loipf]

Hi,
for SNVs, one can easily calculate confidence intervals for the dN/dS ratios per gene using the geneci(), which is really useful. However, it only calculates confidence intervals for SNV classes. Is there an easy way to also calculate confidence intervals for INDELs with observed/expected ratios or does it need a different underlying statistical model?
Thanks in advance.

[676lql]

Hi，I have the same question as you, have you solved your problem yet?

[loipf]

No, but I found a paper that implemented confidence intervals for indels and even came up with a statistical test to compare which genes are different under selective pressure between two populations. Unfortunately, they do not share their code and I am not able to re-implement it.

Zhu, Bin et al. “Comparison of somatic mutation landscapes in Chinese versus European breast cancer patients.” HGG advances vol. 3,1 100076. 3 Dec. 2021, doi:10.1016/j.xhgg.2021.100076
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8756551/

[676lql]

Well, let's pray that the author will help us. ORZ