diff --git a/Snake.config.json b/Snake.config.json
index 636c4296b1de817e561112c27c68b280af3bf151..98afdad1c9c6e534e4eaec1d4fb32891e4aad4b7 100644
--- a/Snake.config.json
+++ b/Snake.config.json
@@ -9,8 +9,6 @@
     "sce_script"    : "/g/korbel/meiers/tools/mosaicatcher/strandsequtils/sce_utils/SCE.R",
     "samtools"      : "samtools",
     "bcftools"      : "bcftools",
-    "class_script"  : "finalCall_cmd.R",
-    "class_dir"     : "/g/korbel/meiers/tools/mosaicatcher/strandsequtils/maryamCode",
 
 
     "exclude_file"  : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher/data/exclude/hg19.exclude",
diff --git a/Snakefile b/Snakefile
index 820cc26465b910024a9dbacef1f484b70cfaf095..3723b7fe86a349a112d7db4cb0fe8757ade546eb 100644
--- a/Snakefile
+++ b/Snakefile
@@ -159,8 +159,6 @@ rule run_sv_classification:
         outdir = "sv_probabilities/" + config["sample"] + ".{windows}.{bpdens}/",
         out1   = "sv_probabilities/" + config["sample"] + ".{windows}.{bpdens}/allSegCellProbs.table"
     params:
-        class_dir     = config["class_dir"],
-        class_command = "Rscript " + config["class_dir"] + "/" + config["class_script"],
         windowsize    = lambda wc: wc.windows.split("_")[0]
     shell:
         """