Using HapNe_IBD on ancestry filtered IBD segments

[sam-sacco]

Hello, I was wondering whether any adjustments to the HapNe-IBD algorithm are needed to make it compatible with local ancestry filtered IBD segments? I'm imagining using the browning pipeline for ASIBDNe to generate ancestry filtered IBD files and then specifying the ancestry specific number of diploid pairs as they describe in the nb_samples line of the config file. Is there anything I'm missing that would make HapNe incompatible with an ancestry specific approach?

[rmnfournier]

From a technical perspective, the method should work with any IBD file or histogram provided. I have not thought a lot about ancestry-filtered IBD segments. A potential issue is that the current implementation considers the length of the chromosomes (src/hapne/regions_X.txt). I wonder if these lengths should be adapted to reflect the expected genome fraction per ancestry.