diff --git a/scripts/gatk_genotyper.py b/scripts/gatk_genotyper.py
index <HASH>..<HASH> 100644
--- a/scripts/gatk_genotyper.py
+++ b/scripts/gatk_genotyper.py
@@ -53,8 +53,7 @@ def unified_genotyper(picard, align_bam, ref_file, platform, dbsnp=None):
     params = ["-T", "UnifiedGenotyper",
               "-I", align_bam,
               "-R", ref_file,
-              "-varout", out_file,
-              "-vf", "VCF",
+              "-o", out_file,
               "--genotype_model", "JOINT_ESTIMATE",
               "--base_model", "EMPIRICAL",
               "--standard_min_confidence_threshold_for_calling", "10.0",
Update output file commands for unified genotyper to match GATK changes