perf(CNVkit): call filter

tasks/CNVkit.wdl

@@ -50,9 +50,9 @@ task CNVkit {
     
     # Derive each segment's absolute integer copy number, ploidy must be int value
     PURITY=`awk -F'\t' '{print $6}' ${hrd} | sed -n '2p'`
-    cnvkit.py call ${sample}.cns -y -m clonal --purity $PURITY -o ${sample}.call.cns
-    cnvkit.py call ${sample}.cnr -y -m clonal --purity $PURITY -o ${sample}.call.cnr
-
+    cnvkit.py call --drop-low-coverag --filter ci ${sample}.cns -y -m clonal --purity $PURITY -o ${sample}.call.cns
+    cnvkit.py call --drop-low-coverag --filter ci ${sample}.cnr -y -m clonal --purity $PURITY -o ${sample}.call.cnr
+    
     # Plot the results
     cnvkit.py scatter ${sample}.cnr -s ${sample}.call.cns -o ${sample}.scatter.pdf
     cnvkit.py diagram ${sample}.cnr -s ${sample}.call.cns -o ${sample}.diagram.pdf