I am calling variants compared to a given genome. I'm finding that using samtools mpileup or bcftools mpileup, I only get reports after there is some nonzero depth of coverage.
Further, I'm finding that if there is a mismatch within the first 5 or so nucleotides, that they will be skipped altogether.
I am hoping that if I can set a minimum depth of coverage to be 0, I will see these skipped regions. Further, I'm hoping that I will see the variant called in those skipped regions, too.
As far as I can tell, samtools/bcftools mpileup only allows you to set a maximum depth of coverage, not a minimum. Is there another tool I could use for this or a parameter I can set for either of these?