Difficulties for running GAEseq

[ebattistella]

Dear authors,
Thank you for releasing this interesting tool. We are currently trying to reproduce the test results in the published article (and aim to then run this tool on real data); however, we are facing several difficulties.

1. We haven’t found in your GitHub a trained model we could use to run the tool. Could you please point us to the trained model?
2. In addition, it seems that the code in the repository runs in training mode (following the steps in the README). Could you please indicate how to run the code in inference mode only given the trained model?
3. Finally, the ExtractMatrix code used to build the SNP matrices uses FASTA and sam files as input, and appears to call SNPs using a threshold. However, we have SNPs already called using dedicated variant calling software. Is it possible to use your code with VCF files?