Hi Peter, Thanks for the flag value and filed issue. ha...66% vs 86% mapping rate to me is not slightly different though...might be I should go with mem
Daofeng On Wed, Oct 29, 2014 at 11:13 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > 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
