samtools mpileup -B or -E
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6.1 years ago
user230613 ▴ 330

Hi there,

I want to do a variant calling analysis using samtools mpileup and I'm wondering about the meaning of two arguments: -B and -E. I've read the documentation about them, and I've more or less understand whats the meaning of BAQ measure. But I am not quite sure whether I should use -B or -E to adjust the call and make it more accurate, I mean, increase specificity without loosing much sensitivity.

Any help would be appreciated.

samtools mpileup variant_calling • 1.6k views