Hi all,

I am searching for snv in virus for some researches. I am using bcftools to call all positions with all nucleotides at each position (even ones let say with only dp=1 ,i want to have them all) and then based on the format i filter out those that aren't present with at least 5 forward reads 5 reverse reads(aligned to ref genome) and 1% presence in snv. I am hoping that with these parameters i can tell that snp is present at some location. Is this ok or i should put even stricter rules? Any other suggestion or someone has already done it on some other way?

Thanks