Yes - with Sequence-based Genotyping or RADSeq you use sequencing machines for genotyping The upsides of using genomic or RAD reads compared to array-based is

Yes - with Sequence-based Genotyping or RADSeq you use sequencing machines for genotyping The upsides of using genomic or RAD reads compared to array-based is that you don't need to make an array first, and sequencing reads is still more expensive than using an array; but with an array you get a more complete set of called genotypes, and you don't get problems with any eventual bad-quality read library. Nevertheless, at some point we'll drop array-based genotypings.