Hi Margaret, The short (unhelpful) answer is that "samtools idxstats" does not decide this - it just reports the numbers already recoded in the *.bai index file (see the SAM/BAM specification for where these numbers are held).
The numbers would be computed by "samtools index" where the FLAG determines if a read is mapped (as per the specification). Unmapped but placed reads are also counted (they have a POS and RNAME, but their FLAG says unmapped - typically used for the unmapped partner of a mapped read as per best practises in the SAM/BAM specification, in order to keep the reads near each other in the file). Unmapped reads with no coordinates get counted against the final dummy "*" reference line shown in "samtols idxstats". Peter On Fri, Feb 26, 2016 at 11:07 PM, Margaret Linan MPH <mli...@asu.edu> wrote: > Hi- > > Does anyone know how IDXSTATS decides that a read is mapped, unmapped > and off-target? Does it only pay attention to the flags in the sam file? > > Thank you, > Margaret > > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help > ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
