Hi Andreas,
On Fri, 2014-11-21 at 10:58 +0800, Andreas Wilm wrote: > Hi all, > > I have a read pair with partial, perfect overlap. In a pileup the > base-qualities for (apparently) one read get bumped up, but the other > is set to zero. With 'mpileup -x' you obviously can't see this. If the > goal of the overlap detection is to merge base-qualities, wouldn't it > make sense to report the merged quality only? ideally yes. The current overlap detection is a bit of a hack which effectively disables overlapping bases by setting one of them to zero. This is required for computing genotype likelihoods in calling, but I understand it brings problems in other uses. Petr > Otherwise programs > reading the output might assume that there was in fact a base with BQ > 0. See below for a small example. Also, is the read overlap detection > documented somewhere? > > Andreas > > > # not paired > # > https://dl.dropboxusercontent.com/u/4119940/samtools-read-pair-overlap-bq0/nopair.bam > $ samtools0.1.19 mpileup -B -Q 0 -r chr1:69804-69804 nopair.bam > chr1 69804 N 2 Aa DF > $ samtools1.0 mpileup -B -Q 0 -r chr1:69804-69804 nopair.bam > chr1 69804 N 2 Aa DF > > # paired > # > https://dl.dropboxusercontent.com/u/4119940/samtools-read-pair-overlap-bq0/pair.bam > $ samtools0.1.19 mpileup -B -Q 0 -r chr1:69804-69804 pair.bam > chr1 69804 N 2 Aa DF > $ samtools1.0 mpileup -B -Q 0 -r chr1:69804-69804 pair.bam > chr1 69804 N 2 Aa i! > $ samtools1.0 mpileup -x -B -Q 0 -r chr1:69804-69804 pair.bam > chr1 69804 N 2 Aa DF > > > -- 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. ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
