HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph
Fig 7
Graphical representation of the HaploCart inference algorithm.
(A): A variation graph with four embedded haplogroups. Each haplogroup sequence can be reconstructed by walking the appropriate nodes of the graph. Suppose we observe three DNA reads (top left). Read 1 is derived unambiguously from the purple haplogroup. Read 2 is equally likely to have come from the purple or red haplogroup. Read 3 could equiprobably have come from any of the four embedded haplogroups. (B) Based on observation of the reads () we compute the posterior probability
for each embedded haplogroup hk. In this case the haplogroup which maximizes this quantity is the purple one, which becomes the haplogroup assignment for the sample. (C) HaploCart (optionally) reports the proportion of posterior mass which falls on the assigned haplogroup (purple). It then goes up each ontological level of the tree, up to the mt-MRCA, reporting the proportion of posterior mass for all haplogroups within the relevant clade.