Hi Petr,
Thanks for the tip. I tried -Bx, and indeed the base qualities are the
original ones. But for this specific position, the number of bases returned
is the same with -x or without -x. Does running without -x exclude
overlapping read pairs? If so, is there a way to get the original quality
but still exclude overlapping reads when running pileup? I am interested in
the allele counts, but do want to avoid double counting when the paired
reads overlap.
Thanks,
BJ
On Thu, Sep 4, 2014 at 5:07 AM, Petr Danecek <p...@sanger.ac.uk> wrote:
> Hi BJ,
>
> can you try running with -Bx? Overlapping read pairs will have base
> qualities adjusted so that in calling their bases are not counted twice.
>
> Best,
> petr
>
>
> On Wed, 2014-09-03 at 19:36 -0400, BJ Chen wrote:
> >
> > Hi,
> >
> >
> > I am trying the new version samtools 1.0. When I tried to use mpileup
> > to look for some positions, I noticed some strange base quality
> > scores. For example:
> >
> >
> > When I do
> >
> >
> > samtools mpileup -B -f h37_hg19.fa -r chr22:17538719-17538719 -q 0 -Q
> > 0 test.bam
> >
> >
> > I get
> >
> > [mpileup] 1 samples in 1 input files
> > <mpileup> Set max per-file depth to 8000
> > chr22 17538719 T 13 <>,.,...,,.,, JIFbF=aIE!I!H
> >
> >
> >
> > Removing -B gives the same results. These quality scores are not the
> > original base quality scores in the bam file. Also, "!" (phred+33),
> > "a" and "b" (phred+64) all appear. The original sequence is Phred+33.
> > Does samtools mpileup still make some changes to the base quality,
> > even though I specific -B (or --no-BAQ)? Is there a way to turn off
> > this option?
> >
> >
> >
> >
> >
> > Thanks,
> > BJ
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Slashdot TV.
> > Video for Nerds. Stuff that matters.
> > http://tv.slashdot.org/
> > _______________________________________________
> > Samtools-help mailing list
> > Samtools-help@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/samtools-help
>
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
------------------------------------------------------------------------------
Slashdot TV.
Video for Nerds. Stuff that matters.
http://tv.slashdot.org/
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
