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
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