diff --git a/advntr/advntr_commands.py b/advntr/advntr_commands.py
index 707466c..76e9966 100644
--- a/advntr/advntr_commands.py
+++ b/advntr/advntr_commands.py
@@ -79,6 +79,8 @@ def genotype(args, genotype_parser):
 
     input_file = args.alignment_file if args.alignment_file else args.fasta
     input_is_alignment_file = input_file.endswith('bam') or input_file.endswith('sam') or input_file.endswith('cram')
+    if not input_is_alignment_file:
+        print_error(genotype_parser, "The input file format is not supported. Please use BAM/CRAM files.")
     working_directory = args.working_directory + '/' if args.working_directory else os.path.dirname(input_file) + '/'
 
     log_file = working_directory + 'log_%s.log' % os.path.basename(input_file)