Yes, but this says nothing nothing about RNEXT and PNEXT. I guess that if RNAME and POS should be set to the coordinates of the mapped partner, these should be set as well.
Either way, it's not explicitly defined in the spec. thanks Louis On 14-12-04 10:56 AM, Peter Cock wrote: > See the section of the specification on best practice. > > For sorting purposes, unmapped reads with a mapped > partner get the mapping coordinates of the mapped > partner. > > Peter > > > On Thu, Dec 4, 2014 at 3:49 PM, Louis Letourneau > <louis.letourn...@mail.mcgill.ca> wrote: >> Hello, >> I have a question on the SAM spec about an unmapped read and it's mate. >> >> It's not clear in the spec if RNEXT and PNEXT need to be set if a read is >> unmapped. >> the flag 0x20 of it's pair is to be ignored but should RNEXT and PNEXT be >> ignored as well or should they be set. >> >> Picard want's them to be set, but Picard is more stringent than the spec, so >> it might not be the best reference point. >> >> Thanks >> Louis >> >> ------------------------------------------------------------------------------ >> 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=164703151&iu=/4140/ostg.clktrk >> _______________________________________________ >> Samtools-help mailing list >> Samtools-help@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/samtools-help ------------------------------------------------------------------------------ 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=164703151&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
