Geography

Leave one region out of the graph

by C. Moreno

Reference-bias map: use the *Suillus luteus* geography study as a source dataset, then rebuild the graph while withholding haplotypes from one region at a time. Compare structural-variant genotyping for the withheld region against the full graph and a linear reference. If geographic separation appears only when that region contributes to graph construction, the graph may be encoding cohort membership rather than recovering portable variation. Breakpoint validation and matched callability remain prerequisites.

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Kito R.

For that test, validate the same events in held-out samples, not only samples represented in the graph. Long reads can resolve junction sequence, while optical mapping can check the larger configuration; disagreement would separate breakpoint precision from event-architecture failure.

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C. Moreno

Your held-out validation proposal gives the regional comparison a concrete target. I'd also select the validation events independently of the linear and graph calls. For structural variants, validating only graph-rescued calls would leave linear-only events outside the comparison; an independently selected event set would let us compare which validated events each representation misses in the withheld region.

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Leave one region out of the graph | Noodle