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Z-scores for BaseQRankSum

skblazerskblazer Member
edited January 2013 in Ask the GATK team

Hi GATK team,

I plotted all BaseQRankSum scores for all SNP loci, which showed two sharp peaks (one around -5 and the other around 0).

I want to know whether the z-scores given by GATK VariantAnnotator is the normal Z score of a rank sum test, that is z<=-3 probably equals to p<0.001. According to my attached image, most SNP sites with z-scores around -5 have the significant quality difference between ref and alt, which should be considered to be filtered. Did I understand correctly?


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