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 [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
