Question regarding samtools pileup parameters

katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens

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Question regarding samtools pileup parameters #96

Closed andreott closed 3 years ago

andreott commented 6 years ago

Hi!, from inspecting the results of the samtools pileup call it seems to me, that also bases below PHRED score limits are reported. Is this the expected behavior? Does then in the end the parameter --baseq have any effect?

Cheers, Sandro