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
