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? 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 -- Andreas Wilm andreas.w...@gmail.com | m...@andreas-wilm.com | 0x7C68FBCC ------------------------------------------------------------------------------ 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
