I dont no

I've done it, starting with structure formatted files.

I mean that I started with Structure formatted files, and then working from those I did a series of search and replace steps in excel to create files that could be read in BGC. I had to use a different series of steps for the hybrid and parental files, as the parental files want only counts of the number of instances of each allele in the population, whereas the hybrids file contains the count of the numbers of each allele in each individual.

Regarding the genotype uncertainty, the counts of each allele are not the number of times that allele occurs in an individual, they are the counts of the number of reads (i.e. number of times the allele was sequenced in a Next Gen Sequencing platform).

Hi, Christopher,

Can you let me know how to plot probability of ancestry against Hybrid index ?

I'm confused by your question. Are you wanting to plot a the genotypes at a particular locus against the hybrid index for different individuals? This is not a figure that BGC produces, but you could do it in R or in MS Excel. 

to plot genomic cline at each locus against the hybrid index

This is a bit late to this thread, but I have been working on a R-package which includes tools to edit and manipulate genomic data. I have a function which will convert directly from a 'GENEPOP' formatted file to the parental (2) and admixed (1) files required by BGC. From our preliminary trials the conversion appears to work, and is quite easy to implement. Links to the package and example use of genepop_bgc included. 

https://github.com/rystanley/genepopedit

https://github.com/rystanley/genepopedit#genepopbgc