Daniel:Notebook/Haplotyping/ConsistentPairs

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Revision as of 18:21, 11 December 2015 by >Djacobse (→‎The Method)
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Comparing Haplotypes Using the Consistent Pairs Method

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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.

File:ConsistentPairs.png

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).