[Samtools] Dp4 Vs. Dp: Low-Quality Bases Not Counted
1
2
Entering edit mode
11.2 years ago
jomaco ▴ 200

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

samtools quality • 3.4k views
ADD COMMENT
4
Entering edit mode
11.2 years ago
pd3 ▴ 350

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

ADD COMMENT

Login before adding your answer.

Traffic: 1632 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6