[Samtools-help] rmdup question

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Dear Samtools community,

I have a problem with rmdup I hope you can help me. I am working with paired-end data (samtools 1.3.1), I sort my file and then after using rmdup I use flagstat to check the number or reads and I see that single reads were eliminated not only pairs, I did not add any other option. I could just use "fixmate" to continue but I do not understand what is happening. It might be also important to note that before doing this I use "fixmate" to check everything is paired properly.

Regards