[Samtools] Dp4 Vs. Dp: Low-Quality Bases Not Counted

Question

[jomaco]

Hi,

In the samtools manual, for the DP4 field it states that the:

"...sum can be smaller than DP because low-quality bases are not counted."

I wonder, what is the cut-off for this? How low does the quality of a base need to be and what determines whether a base is low-quality?

Thanks,

Jon

Answer 1

[pd3]

This is the mpileup -Q option, which by default is 13.