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
