Commands to Generate Summary Statistics in summary.html

[assia-hub]

Hello,

I am trying to replicate the summary.html file generated by SnpEff and am having difficulty matching the statistics presented. Specifically, I am interested in understanding the exact commands and filters used to generate the report, including:

Number of variants (before filter): 19,606,739
Number of variants processed (after filter and non-variants): 18,949,050
Could you please provide a detailed list of the commands used to generate this file, along with any specific filters or settings applied to obtain these statistics?

Thank you very much for your help.

version : snpeff/5.1