Symmetric Odds Ratio to detect strand bias

Category Variant Annotations

VCF Field INFO (variant-level)

Type ActiveRegionBasedAnnotation


Odds Ratios in the 2x2 contingency table below are R = (X[0][0] * X[1][1]) / (X[0][1] * X[1][0]) and its inverse + strand - strand Ref X[0][0] X[0][1] Alt X[1][0] X[1][0] The sum R + 1/R is used to detect a difference in strand bias for ref and for alt (the sum makes it symmetric): A high value is indicative of large difference where one entry is very small compared to the others.

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GATK version 3.2-2-gec30cee built at 2014/09/12 22:29:29. GTD: NA