See the Picard FAQ: http://sourceforge.net/p/picard/wiki/Main_Page/#q-why-am-i-getting-errors-from-picard-like-mapq-should-be-0-for-unmapped-read-or-cigar-should-have-zero-elements-for-unmapped-read
-Alec On 7/31/14, 4:36 AM, Wolfgang Maier wrote: > Hi, > > I've tried to run SamToFastq on a sam file with unaligned reads. Right > on the first line picardtools complains: > > Exception in thread "main" > htsjdk.samtools.SAMFormatException: Error parsing text SAM > file. MAPQ must be zero if RNAME is not specified; Line 4 > Line: > HWI-EA332_1_2_662_117/1 4 * 0 255 * * > 0 0 > CCACACTACACCCTAACACACCCTAATCTAACCCTGGCCAACCTGTCTCTC > BBBBCCCCBB@BCB?CBC@ABB?<>AB?CBCBB@BC>BB@BB7BCB<BCA? RG:Z:007 > > After consulting the sam format specifications I think that this > behavior is incorrect. > The read has bit 4 set in the FLAG field and with that "no assumption > can be made about RNAME, POS, CIGAR, MAPQ", so picard shouldn't even > look at MAPQ here. > Even if it did, I don't know whether it should expect MAPQ to be zero in > the absence of RNAME as a MAPQ value of 255 "indicates that the mapping > quality is not available", which seems to be about as reasonable as > setting it to 0. > > Please correct me if I'm getting this wrong, > Wolfgang > > > ------------------------------------------------------------------------------ > Infragistics Professional > Build stunning WinForms apps today! > Reboot your WinForms applications with our WinForms controls. > Build a bridge from your legacy apps to the future. > http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help ------------------------------------------------------------------------------ Infragistics Professional Build stunning WinForms apps today! Reboot your WinForms applications with our WinForms controls. Build a bridge from your legacy apps to the future. http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
