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brentp / bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
https://arxiv.org/abs/1401.1129
MIT License
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Unique mapped reads #81

Open Hongxiang2023 opened 2 years ago

Hongxiang2023 commented 2 years ago

Hi,

I'm just curious how the unique mapped reads are counted? Is it using the mapping quality or XA and SA tag to filter out the reads? Thank you!!

brentp commented 2 years ago

Hi, it uses the sam flag to determine primary and it only counts primary, not secondary or supplemental reads.