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Old 08-07-2014, 06:46 AM   #3
Junior Member
Location: DC

Join Date: Aug 2014
Posts: 3

@swbarnes, thanks for the quick reply. That certainly explains what I am seeing. I inspected a larger sample and found SAMtools v01.19 is indeed filtering out the read bases with quality < 13.

Interesting that SAMtools 0.1.18 is not behaving the same as v0.1.19. Both versions mpileup usage show this:

-Q INT skip bases with baseQ/BAQ smaller than INT [13]
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