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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
141 stars 54 forks source link

unique bam? #57

Closed MoutonAlice closed 5 years ago

MoutonAlice commented 5 years ago

Hi many thanks for developing this tools, it is super fast! I have a question. Do bwa-meth output unique mapping reads or should I add an additional filter? Many thanks for your help Alice

brentp commented 5 years ago

glad to hear it's useful. it does not mark duplicates. you'll have to do that outside of bwa-meth.