Hi all,
I'm trying to work out ancestry proportions for individuals sampled from a hybrid zone using ultra low coverage WGS data. I have been playing around with the NgsAdmix program (http://www.popgen.dk/software/index.php/NgsAdmix) and I noticed there is an option to specify genotype frequencies for the ancestral populations (using the flag -fname) but there is no information on the website or tutorial page about how to do this, or what format the ancestral genotype frequencies should be in. Does anyone know how to do this?
I have actually already calculated ancestral genotype frequencies using higher-coverage data from individuals already assigned to the ancestral populations. I did this using WGSassign (https://github.com/mgdesaix/WGSassign?tab=readme-ov-file) with the -get_reference_af option, which outputs a numpy binary file. Can I extract and use this data for NgsAdmix in some way, or is there a better option for calculating the ancestral frequencies?
Any help/advice would be much appreciated.
J.
