Using other reference genome builds

[mhSepehri]

Is there any way to use reference genomes of organisms other than hg19, hg38, mm9, and mm10?

I am trying to use facets for dog samples (canFam3) and the first part of generating pileup file works fine and creates an output with all 38 + x chromosomes output.csv.gz, but it cannot produce final results correctly.