When I accidentally passed the wrong BED file to trgt genotype, it completed successfully after outputting an error message for every locus like
....
[ERROR] - Locus processing: Error at BED line 9: Expected 4 fields in the format 'chrom start end info', found 5: chr1 52256 52303
...
I think it would be more intuitive if it ran the validate subcommand internally before starting to genotype.