How to Get Nucleotide/Allele Frequency Spectrum From NGS SAM/VCF File

Question

[liaoyunshi]

Dear All,

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!

Best LYS