I would like to ask the same thing. A bit more specifically, I gathered that, without the option, samtools recalculates the quality scores in the output to, effectively, ignore one of the two reads. What I didn't find information on is what consequences this would have for reported coverage in the DP and DPR fields of final vcf output. Would overlapping reads still contribute twice to these ?
Thanks, Wolfgang On 04/14/2015 03:10 PM, Dario Beraldi wrote: > Hello, > > In samtools v.1.1 mpileup takes the option "-x --ignore-overlaps" which > is described as "disable read-pair overlap detection". Could anyone > clarify what this means? > > My guess/understanding is that overlapping read pairs are not double > counted when the mates overlap, unless -x is set. Is this correct? > > In previous versions overlapping read pairs were instead double counted, > right? > > Thanks > Dario > > > ------------------------------------------------------------------------------ > BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT > Develop your own process in accordance with the BPMN 2 standard > Learn Process modeling best practices with Bonita BPM through live exercises > http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ > source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF > > > > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help > ------------------------------------------------------------------------------ One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
