Daniel:Notebook/Haplotyping/ConsistentPairs: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Djacobse
(Created page with "=Comparing Haplotypes Using the Consistent Pairs Method= Back to Notebook ==The Method== The consistent pairs method is derived from the [ht...")
 
>Djacobse
Line 8: Line 8:


[[Image:ConsistentPairs.png|800px]]
[[Image:ConsistentPairs.png|800px]]
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).

Revision as of 18:21, 11 December 2015

Comparing Haplotypes Using the Consistent Pairs Method

Back to Notebook

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).