I am new to NGS related analysis, so could you help me solve this question?
I have SAM file from the NGS result of a virus popultion. Then I want get a summary of the Non-consensus variant frequency spectrum for the population, just like the panel B of (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3647518/figure/F2/) shown.
So I want to know if there is any tools can generate this kind of plot, or can generate raw data that include the Non-consensus variant frequency site by site along the genome?
Many thanks for your kindness!