On Wed, Oct 29, 2014 at 4:01 PM, Daofeng Li <lid...@gmail.com> wrote: > Hi Alec, > > Yes, somehow I also found this right after I sent out the email.... > So if I want to filter this kind of alignment out, is there a flag could > use?
Yes, use the 0x800 FLAG bit value, e.g. samtools view with the -f or -F options can filter for supplementary reads. > I am still wondering the big difference between mapped reads count? They are two very different mapping algorithms so are expected to give slightly different output. > btw, the 'supplimentary' word in flagstat output, is a typo? > > Thanks for response. Yes, well spotted - I filed a pull request to get that fixed: https://github.com/samtools/samtools/pull/311 Peter ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
