I have a vcf file from whole genome data on a fish species. This vcf file has prepared with bcftools pipeline. I have read something for filtering the vcf file but I couldn't make heads or tails of them. I know there is GATK pipeline but because I used bowtie2 for mapping I am not able to use that pipeline, I think. So I will be so grateful if you can help to filter my vcf file with bcftools or vcftools or any other ways.
Any help will be appreciated in advance.