diff --git a/Snakefile b/Snakefile
index def2ad7c59e5ed480dd83ee06a25fe9dd8c6a726..c61fecf3f398a634e14bffa1f3ab0f086b3d235a 100644
--- a/Snakefile
+++ b/Snakefile
@@ -304,9 +304,7 @@ rule mosaiClassifier_make_call:
     output:
         "sv_calls/{sample}/{windows}.{bpdens}/simpleCalls.txt"
     shell:
-        """
-        Rscript utils/mosaiClassifier.makeCall.R {input} {output}
-        """
+        "utils/mosaiClassifier_call.snakemake.R"
 
 rule mosaiClassifier_calc_probs:
     input:
diff --git a/utils/mosaiClassifier_call.snakemake.R b/utils/mosaiClassifier_call.snakemake.R
new file mode 100644
index 0000000000000000000000000000000000000000..efc74e2ba421a50803d0756d80ace201dfbf2e8a
--- /dev/null
+++ b/utils/mosaiClassifier_call.snakemake.R
@@ -0,0 +1,9 @@
+library(data.table)
+source("utils/mosaiClassifier/makeSVcalls.R")
+
+probs = readRDS(snakemake@input[["probs"]])
+llr   = as.numeric(snakemake@params[["llr"]])
+
+tab <- makeSVCallSimple(probs)
+
+write.table(tab, file = snakemake@output[[1]], sep = "\t", quote=F, row.names = F, col.names = T)