diff --git a/bcbio/variation/genotype.py b/bcbio/variation/genotype.py
index <HASH>..<HASH> 100644
--- a/bcbio/variation/genotype.py
+++ b/bcbio/variation/genotype.py
@@ -45,6 +45,8 @@ def _shared_gatk_call_prep(align_bams, ref_file, config, dbsnp, region, out_file
     params = ["-R", ref_file,
               "--standard_min_confidence_threshold_for_calling", confidence,
               "--standard_min_confidence_threshold_for_emitting", confidence,
+              "--downsample_to_coverage", "250",
+              "--downsampling_type", "BY_SAMPLE",
               ]
     for a in annotation.get_gatk_annotations(config):
         params += ["--annotation", a]
Provide standard downsampling during GATK variant calling to match <I> defaults on older versions: <I>bp per sample downsampling