diff --git a/bcbio/variation/recalibrate.py b/bcbio/variation/recalibrate.py
index <HASH>..<HASH> 100644
--- a/bcbio/variation/recalibrate.py
+++ b/bcbio/variation/recalibrate.py
@@ -96,12 +96,14 @@ def _gatk_base_recalibrator(broad_runner, dup_align_bam, ref_file, platform,
     """Step 1 of GATK recalibration process, producing table of covariates.
     """
     out_file = "%s.grp" % os.path.splitext(dup_align_bam)[0]
+    plot_file = "%s-plots.pdf" % os.path.splitext(dup_align_bam)[0]
     if not file_exists(out_file):
         if has_aligned_reads(dup_align_bam):
             with curdir_tmpdir() as tmp_dir:
                 with file_transaction(out_file) as tx_out_file:
                     params = ["-T", "BaseRecalibrator",
                               "-o", tx_out_file,
+                              "--plot_pdf_file", plot_file,
                               "-I", dup_align_bam,
                               "-R", ref_file,
                               ]
Enable writing of GATK recalibration plots to replace old custom plots