Hello I am using bcftools to call variants with this command:
bcftools mpileup -Ou -b bamlist -f ref.fasta | bcftools call -Ob -mv >variant.bcf
However, for some specific variants that I know to exist (looking at bam files with IGV), I do not get variant calls. The read depth is shallow 3-4 reads per site. How do I force bcftools to output all possible variants, even tough they have low probability?