Hi John, Samtools and picard use very similar algorithms. The major difference IIRC is that picard’s MarkDuplicates works for inter-chromosomal pairs whereas samtools restricts itself to pairs where both ends map to the same chromosome for performance reasons.
-t On Sep 22, 2014, at 5:07 PM, John Duce <john.d.d...@gmail.com> wrote: > Dear Samtools Gurus, > > I did a lot of googling and looking through the code but I couldn't find > anything definitive about my question. It is my understanding that samtools > rmdup removes duplicates based on position only, whereas picard > MarkDuplicates marks duplicates based on position and sequence. Is this > correct? > > John Duce > ------------------------------------------------------------------------------ > Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer > Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports > Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper > Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer > http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk_______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help ------------------------------------------------------------------------------ Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
