Hi Xiao,
Those flags explicitly indicate that the alignments are properly paired.
The non-properly paired versions of those would be 65 and 129. You may find
the "Explain SAM flags" page useful:
https://broadinstitute.github.io/picard/explain-flags.html
Best,
Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Laboratory for Molecular and Cellular Cognition
German Centre for Neurodegenerative Diseases (DZNE)
Ludwig-Erhard-Allee 2
53175 Bonn
Germany
<devon.r...@dzne.de>
On Mon, Feb 9, 2015 at 7:08 PM, Xiao Li <lixia...@gmail.com> wrote:
> 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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look and join the conversation now. http://goparallel.sourceforge.net/
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