Implement variant finding for species without reference VCF

[acesnik]

There are many cases where Ensembl has the reference genome and gene model, but no reference VCF. We could consider using the recommended GATK pipeline for non-human genomes.

And if it turns out that there is as yet no suitable set of known sites for your organisms, here's how to make your own for the purposes of BaseRecalibration: First, do an initial round of SNP calling on your original, unrecalibrated data. Then take the SNPs that you have the highest confidence in and use that set as the database of known SNPs by feeding it as a VCF file to the base quality score recalibrator. Finally, do a real round of SNP calling with the recalibrated data. These steps could be repeated several times until convergence. Good luck!

https://gatkforums.broadinstitute.org/gatk/discussion/1247/what-should-i-use-as-known-variants-sites-for-running-tool-x

Those tools are already implemented in the pipeline, so it'd just be reordering them and doing this iterative approach within variants.smk.