Dear samtools developer,
Thank you for developing samtools! It is a very useful tool for my research!
I just have a quick question relevant to flagstat and it is very likely
that I misunderstood something. I realized that it actually classifies
reads with flag 67 and 131 as the "properly paired" reads in the report.
However, my understanding is that they are the reads mapped within the
insert size but wrong orientation. Did I misunderstood something here or
used the wrong command (I used samtools flagstat input-bam-file >
output-report) ? Thank you very much for your help!
Best,
Xiao
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