What is the coverage of your bams? samtools samples randomly 255 reads when calculating genotype likelihoods.
petr On Mon, 2016-02-01 at 09:35 -0500, Thomas W. Blackwell wrote: > See option -d, --max-depth. Also -F, -L, -m for indel calling. > > These count all reads overlapping a candidate variant site, rather > than by starting position. > > - tom blackwell - > > On Mon, 1 Feb 2016, Gnter Jger wrote: > > > Dear Samtools-Team, > > I encountered that samtools mpileup followed by bcftools for variant > calling produces different results when the bam file is sorted > differently. Since the bam file has to be sorted by coordinate, the > order of reads sharing the same start position may vary in different > versions of the bam file, i.e. if reads in a coordinate sorted bam file > are shuffled and then sorted by coordinate again, the order of reads > mapping to identical start positions usually differs from the order of > the same reads in the initial bam file. > > This however, does change the quality of the variants that are called by > bcftools. Is suspect that the genotype likelihoods change. I would have > expected that changing the order of reads mapping to the same start > position does not influence the variant calling, when using the exactly > same samtools mpileup/bcftools commands. I use the current version 1.3., > but also older versions show that problem. > > Is there any explanation why this is the case? The problem occurs with > every bam file I tested so far. It seems like samtools mpileup does not > use all of the reads overlapping a variant position for likelihood > estimation?! Is there any option in bcftools or samtools mpileup to > prevent this from happening, i.e. to produce the same variant quality > scores/genotype likelihood values regardless of the order of reads? > > I would appreciate any comments on that. > > Best regards, > Günter > > ------------------------------------------------------------------------------ > 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=267308311&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=267308311&iu=/4140 > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ 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=267308311&iu=/4140 _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
