diff --git a/Snake.config.json b/Snake.config.json
index 89ed2b4257211b0565a9c770e5fe334f69224256..5091f0958b4ebbca54fb17759044039df0b39d6b 100644
--- a/Snake.config.json
+++ b/Snake.config.json
@@ -4,7 +4,6 @@
     "reference"     : "/MMCI/TM/scratch/ref/GRCh38_no_alt_analysis_set/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna",
     "mosaicatcher"  : "/MMCI/TM/scratch/strandseq/mosaicatcher-builds/v0.3/build/mosaic",
     "plot_script"   : "/MMCI/TM/scratch/strandseq/mosaicatcher-builds/v0.3/R/qc.R",
-    "norm_script"   : "/MMCI/TM/scratch/strandseq/mosaicatcher-builds/v0.3/R/norm.R",
     "samtools"      : "samtools",
     "bcftools"      : "bcftools",
 
diff --git a/Snakefile b/Snakefile
index 810e59a556789e57b2fd91aab60e711e2b62892d..3c35f68c38de778bbba35b2dcd5ac200ccc0be43 100644
--- a/Snakefile
+++ b/Snakefile
@@ -436,11 +436,9 @@ rule normalize_counts:
         "counts/{sample}/{window}_fixed_norm.txt.gz"
     log:
         "log/normalize_counts/{sample}/{window}_fixed.log"
-    params:
-        r_command = config["norm_script"]
     shell:
         """
-        Rscript {params.r_command} {input.counts} {input.norm} {output} 2>&1 > {log}
+        Rscript utils/normalize.R {input.counts} {input.norm} {output} 2>&1 > {log}
         """
 
 rule link_normalized_info_file: