Discrepancy between graph length, reference length, and novel base pairs about panacus HOT 3 CLOSED

Thank you for your quick response, It seems I misunderstood the function of the subset and exclude options. I reran the analysis and all the numbers check out. Thanks again for your help.

from panacus.

From your code, it looks like you exclude GRCh38, and compute growth for the subset, omitting GRCh38 and CHM13. Then you reason about the size of the total graph, but taking CHM13 as baseline. Even if your subset omits CHM13, it still counts nodes/bps covered by CHM13 if they are covered also by haplotypes of the subset. So this is the difference between exclude and subset: The exclude option makes sure that no bp of the specified paths is ever counted, while the subset option does count bps covered by the subset.

from panacus.

In other words, if you exclude CHM13 rather than GRCh38, this should check out.

from panacus.