更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -4,6 +4,7 @@ task cnvkit{
     File ref_dir
     String? fasta
     File ref_flat
+    File hrd
     File tumor_bam
     File tumor_bam_index
     File? normal_bam
@@ -21,17 +22,28 @@ task cnvkit{
         
         echo ${sample}
 
-        /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} -n ${normal_bam} -m wgs -f ${ref_dir} --annotate ${ref_flat} --diagram --scatter -p $nt
+        /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} -n ${normal_bam} -m wgs -f ${ref_dir} --annotate ${ref_flat} -p $nt
 
-        #/root/miniconda2/bin/cnvkit.py scatter ${sample}.cnr -s ${sample}.cns -o ${sample}_scatter.pdf
+                  
+        # Check noise
+    	/root/miniconda2/bin/cnvkit.py metrics ${sample}.cnr -s ${sample}.cns > ${sample}.stats
+    
+        # Derive each segment's absolute integer copy number, ploidy must be int value
+        PURITY=`awk -F'\t' '{print $6}' ${hrd} | sed -n '2p'`
+        /root/miniconda2/bin/cnvkit.py segmetrics ${sample}.cnr -s ${sample}.cns --ci -o ${sample}.segmetrics.cns
+        /root/miniconda2/bin/cnvkit.py call ${sample}.segmetrics.cns --drop-low-coverage --filter ci -m threshold --purity $PURITY -o ${sample}.call.cns
+          
 
-        #/root/miniconda2/bin/cnvkit.py diagram ${sample}.cnr -s ${sample}.cns -o ${sample}.diagram.pdf
+        /root/miniconda2/bin/cnvkit.py genemetrics ${sample}.cnr -t 0.2 -m 3 -o ${sample}.ratio_cnv.txt
 
-        /root/miniconda2/bin/cnvkit.py heatmap ${sample}.cnr ${sample}.cns -o ${sample}.heatmap.pdf
+        /root/miniconda2/bin/cnvkit.py genemetrics ${sample}.cnr -s ${sample}.call.cns -t 0.2 -m 3 -o ${sample}.segment_cnv.txt
 
-        /root/miniconda2/bin/cnvkit.py genemetrics ${sample}.cnr -t 0.2 -m 3 -o ${sample}.ratio_cnv.txt
 
-        /root/miniconda2/bin/cnvkit.py genemetrics ${sample}.cnr -s ${sample}.cns -t 0.2 -m 3 -o ${sample}.segment_cnv.txt
+        /root/miniconda2/bin/cnvkit.py scatter ${sample}.cnr -s ${sample}.call.cns -o ${sample}_scatter.pdf
+
+        /root/miniconda2/bin/cnvkit.py diagram ${sample}.cnr -s ${sample}.call.cns -o ${sample}.diagram.pdf
+
+        /root/miniconda2/bin/cnvkit.py heatmap ${sample}.cnr ${sample}.call.cns -o ${sample}.heatmap.pdf
 
         cat ${sample}.ratio_cnv.txt | tail -n+2 | cut -f1 | sort | uniq > ratio_cnv.txt
         cat ${sample}.segment_cnv.txt | tail -n+2 | cut -f1 | sort | uniq > segment_cnv.txt