Which training sets / arguments should I use for running VQSR?
"These recommendations are valid for use with calls generated by both the UnifiedGenotyper and HaplotypeCaller. These recommendations will probably not work properly on calls generated by other (non-GATK) callers."
Read here for more info: https://www.broadinstitute.org/gatk/guide/article?id=1259
So... you can try and check if it works, but taking into account that is not the recommended workflow.