you can compare the VCF files of different conditions: you can check for the common mutations between the conditions you are studying, you can check for the unique mutations for each group...

You could use bcftools filter followed by awk/sed liners. Before you start this,w hat would be your question? what are the inherent sample specifics you are looking into? For example, if you want to have a cutoff for depth, please use the following for depth 20 cutoff bcftools filter -i 'MIN(INFO/DP)>20' filename.vcf > filename_output_DP20.vcf

This could be followed by looking into hom/het calls etc.

The same could also be deployed for csv files as well.

Hope this helps

do I have to analyse vcf population-wise and compare the vcf files of each population for estimating genetic diversity????? And as I have mentioned that I have annotated vcf file that means I had to do further analysis using this annotated file only???

please suggest me how to proceed further. Thank you in advance