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From: Nils H. <nh...@br...> - 2014-09-22 21:18:23
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Hey Siva, based upon my reading reads are ignored in *CalculateHsMetrics* if they are one of secondary, supplemental, fail vendor QC checks, marked as duplicates, zero mapping quality, or unmapped. These are hard-coded at the moment. The relevant code is in the "*acceptRecord*" method in Picard: https://github.com/broadinstitute/picard/blob/master/src/java/picard/analysis/directed/TargetMetricsCollector.java If you have a case that is not in one of the list above, could you please submit a test case for us to look at? Nils On Mon, Sep 15, 2014 at 3:02 PM, Gowrisankar, Sivakumar < siv...@no...> wrote: > Hi All > > > > I target a highly homologous target region of about 300 Kb. I have an > bwa-aligned BAM file that is not marked for duplicates. When I use Picard > to CollectHsMetrics, I find that about 15% of the region is not covered > (using PCT_TARGET_BASES_2X). As far as I know all my regions are covered, > which I checked this with complementary tools such as CallableLoci from > GATK. > > > > My question is does Picard ignore Low/Zero MQ reads while estimating > different metrics? > > > > Thanks > > Siva > > > > > ------------------------------------------------------------------------------ > Want excitement? > Manually upgrade your production database. > When you want reliability, choose Perforce > Perforce version control. Predictably reliable. > > http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk > _______________________________________________ > Samtools-help mailing list > Sam...@li... > https://lists.sourceforge.net/lists/listinfo/samtools-help > > |