bug

codes/public/hotspot/hotspot_delins.bed

@@ -1,3 +1,3 @@
-chr7	55242414	55242513
-chr7	55248985	55249172
-chr17	37880978	37881164
+chr7	55242394	55242533
+chr7	55248965	55249192
+chr17	37880958	37881184

wdl/call_mutation.wdl

@@ -295,12 +295,16 @@ task hotspot {
         fi
 
         # hotspot
-        vcf_filter.py \
-        -i ${raw_vcf} \
-        -e 'INFO/AF[0] < ${threshold}' \
-        -o ${output_dir}/mutation/${name}.raw.hotspot.vcf
+#        vcf_filter.py \
+#        -i ${raw_vcf} \
+#        -e 'INFO/AF[0] < ${threshold}' \
+#        -o ${output_dir}/mutation/${name}.raw.hotspot.vcf
 
-        vcf_operations.py ${output_dir}/mutation/${name}.raw.hotspot.vcf \
+#        vcf_operations.py ${output_dir}/mutation/${name}.raw.hotspot.vcf \
+#        -b $PUBLIC/hotspot/hotspot_delins.bed \
+#        -o ${output_dir}/mutation/${name}.raw.hotspot.delins.vcf
+
+        vcf_operations.py ${raw_vcf} \
         -b $PUBLIC/hotspot/hotspot_delins.bed \
         -o ${output_dir}/mutation/${name}.raw.hotspot.delins.vcf