Daniel:Notebook/Haplotyping/ConsistentPairs
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Comparing Haplotypes Using the Consistent Pairs Method
The Method
The consistent pairs method is derived from the 2013 BMC paper by Matsumoto and Kiryu. The method is a tool for evaluating the consistency of haplotypes. Basically, we can define a consistent pair as one whose SNPs are phased in the same manner (e.g. 00/11 and 00/11). An inconsistent pair is one who has not been phased in a similar manner. For better explanation, see the figure below taken from the 2013 paper.
We can therefore define precision as CP/(CP+IP). The paper also defines recall as the number of pairs found (CP+IP) divided by the total number of pairs available (in the VCF).