diff --git a/python/run_FastQTL_threaded.py b/python/run_FastQTL_threaded.py
index bb5dbfa..ed4e437 100755
--- a/python/run_FastQTL_threaded.py
+++ b/python/run_FastQTL_threaded.py
@@ -28,6 +28,8 @@ def get_cmd(args, chunk):
         cmd += ' --permute '+' '.join([str(p) for p in args.permute])
     if args.seed:
         cmd += ' --seed '+args.seed
+    if args.exclude_samples:
+        cmd += ' --exclude-samples '+args.exclude_samples
     cmd += ' --chunk '+str(chunk)+' '+args.chunks\
         + ' --out '+args.prefix+'_chunk{0:03d}.txt.gz'.format(chunk)\
         + ' --log '+args.prefix+'_chunk{0:03d}.log'.format(chunk)
@@ -56,6 +58,7 @@ def perm_worker(inputs):
 parser.add_argument('--ma_sample_threshold', default='0', help='Include only genotypes with >=ma_sample_threshold samples carrying the minor allele (default 0)')
 parser.add_argument('--fdr', default=0.05, type=np.double)
 parser.add_argument('--seed', default=None, help='Random number generator seed')
+parser.add_argument('--exclude_samples', default=None, help='')
 parser.add_argument('-t', '--threads', default='8', help='Number of threads')
 parser.add_argument('-o', '--output_dir', default='.', help='Output directory')
 args = parser.parse_args()