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I see that old documentation for GATK 1.6 is no longer available (http://gatkforums.broadinstitute.org/discussion/1615/old-doc). I was hoping to find out how the UnifiedGenotyper handled zero-quality mappings. The most recent documentation for 2.x says there is are
"internal quality control metrics (like MAPQ > 17, for example)"
I did not see a command line argument for a min. mapping qual when I ran UnifiedGenotyper (GATK v1.6-7-g2be5704), and I wanted to confirm that the UnifiedGenotyper in version v1.6-7-g2be5704 is ignoring bases from reads with zero mapping qualities for the genotype calculations, (and, perhaps those with mapping quality <= 17, as well). I confess I'm also unsure if zero mapping quality bases are included in the vcf DP field for INFO and/or FORMAT.
Sorry for the extensive question, and thanks for the forum, and for any help you could give.