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Old 01-20-2015, 09:06 AM   #8
Location: San Francisco, CA

Join Date: Aug 2011
Posts: 91

Originally Posted by dpryan View Post
There's no strict definition of high quality, it'll depend on the program used to call the sites (there's no guarantee that a DP4 field will even exist in any given VCF file).
What about samtools | mpileup | bcftools in particular?
I know mpileup has a default base quality of 13 and mapping quality of 0, but that's "raw depth" right?
What does samtools' high-quality mean?
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