IGV

tasks/final_merge.wdl

@@ -3,8 +3,6 @@ task final_merge {
 	File callable_merged_intersect_bed
 	File HR_merged_intersect_bed
 	File variants_merged_bed
-	File bed_10X
-	File PMRA_bed
 	String docker
 	String disk_size
 	String cluster_config
@@ -16,10 +14,6 @@ task final_merge {
 
 		/opt/ccdg/bedtools-2.27.1/bin/bedtools intersect -a variant_invariant.bed -b ${callable_merged_intersect_bed} > benchmark_regions.bed
 
-		cat ${bed_10X} ${PMRA_bed} | cut -f1,14,15 | sort -k1,1 -k2,2n > false.positive.bed
-
-		/opt/ccdg/bedtools-2.27.1/bin/bedtools subtract -a benchmark_regions.bed -b false.positive.bed > benchmark_regions.filtered.bed
-
 		>>>
 
 		runtime {
@@ -31,7 +25,7 @@ task final_merge {
 
 	output {
 		File variant_invariant = "variant_invariant.bed"
-		File benchmark_region = "benchmark_regions.filtered.bed"
+		File benchmark_region = "benchmark_regions.bed"
 	}
 }
 

tasks/remove_IGVrm_bed.wdl

@@ -0,0 +1,37 @@
+task remove_IGVrm_bed {
+	
+	File benchmark_region
+	File bed_10X
+	File PMRA_bed
+	String docker
+	String disk_size
+	String cluster_config
+	
+
+	command <<<
+
+		cat ${bed_10X} ${PMRA_bed} | cut -f1,14,15 | sort -k1,1 -k2,2n > false.positive.bed
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools subtract -a ${benchmark_region} -b false.positive.bed > benchmark_regions.filtered.bed
+
+		>>>
+
+		runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File variant_invariant = "variant_invariant.bed"
+		File benchmark_filtered_region = "benchmark_regions.filtered.bed"
+	}
+}
+
+
+
+
+
+
+

tasks/remove_IGVrm_vcf.wdl

@@ -0,0 +1,73 @@
+task remove_IGVrm_vcf {
+	
+	File benchmark_region
+	File LCL5_annotated_vcf
+	File LCL6_annotated_vcf
+	File LCL7_annotated_vcf
+	File LCL8_annotated_vcf
+	File vcf_info
+	String docker
+	String disk_size
+	String cluster_config
+	
+
+	command <<<
+
+		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${LCL5_vcf} --include-bed=${benchmark_region} -o LCL5.high.confidence.calls.vcf.gz
+
+		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${LCL6_vcf} --include-bed=${benchmark_region} -o LCL6.high.confidence.calls.vcf.gz
+
+		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${LCL7_vcf} --include-bed=${benchmark_region} -o LCL7.high.confidence.calls.vcf.gz
+
+		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${LCL8_vcf} --include-bed=${benchmark_region} -o LCL8.high.confidence.calls.vcf.gz
+
+		zcat LCL5.high.confidence.calls.vcf.gz | grep '#' > LCL5.header
+		zcat LCL6.high.confidence.calls.vcf.gz | grep '#' > LCL6.header
+		zcat LCL7.high.confidence.calls.vcf.gz | grep '#' > LCL7.header
+		zcat LCL8.high.confidence.calls.vcf.gz | grep '#' > LCL8.header
+
+		gunzip LCL5.high.confidence.calls.vcf.gz
+		gunzip LCL6.high.confidence.calls.vcf.gz
+		gunzip LCL7.high.confidence.calls.vcf.gz
+		gunzip LCL8.high.confidence.calls.vcf.gz
+
+		python /opt/annotate_vcf.py -info ${vcf_info} -vcf LCL5.high.confidence.calls.vcf -prefix LCL5
+		python /opt/annotate_vcf.py -info ${vcf_info} -vcf LCL6.high.confidence.calls.vcf -prefix LCL6
+		python /opt/annotate_vcf.py -info ${vcf_info} -vcf LCL7.high.confidence.calls.vcf -prefix LCL7
+		python /opt/annotate_vcf.py -info ${vcf_info} -vcf LCL8.high.confidence.calls.vcf -prefix LCL8
+
+
+		cat LCL5.annotated.txt | awk '{print $1"\t"$2"\t.\t"$4"\t"$5"\t.\t.\tVOTE="$13"\tGT:ALT:DP\t"$10":"$18":"$17}' | cat LCL5.header - > LCL5.high.confidence.calls.annotated.vcf
+		cat LCL6.annotated.txt | awk '{print $1"\t"$2"\t.\t"$4"\t"$5"\t.\t.\tVOTE="$14"\tGT:ALT:DP\t"$10":"$20":"$19}' | cat LCL6.header - > LCL6.high.confidence.calls.annotated.vcf
+		cat LCL7.annotated.txt | awk '{print $1"\t"$2"\t.\t"$4"\t"$5"\t.\t.\tVOTE="$15"\tGT:ALT:DP\t"$10":"$22":"$21}' | cat LCL7.header - > LCL7.high.confidence.calls.annotated.vcf
+		cat LCL8.annotated.txt | awk '{print $1"\t"$2"\t.\t"$4"\t"$5"\t.\t.\tVOTE="$16"\tGT:ALT:DP\t"$10":"$24":"$23}' | cat LCL8.header - > LCL8.high.confidence.calls.annotated.vcf
+
+
+		>>>
+
+		runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File LCL5_filtered_vcf = "LCL5.high.confidence.calls.vcf"
+		File LCL6_filtered_vcf = "LCL6.high.confidence.calls.vcf"
+		File LCL7_filtered_vcf = "LCL7.high.confidence.calls.vcf"
+		File LCL8_filtered_vcf = "LCL8.high.confidence.calls.vcf"
+		File LCL5_annotated_vcf = "LCL5.high.confidence.calls.annotated.vcf"
+		File LCL6_annotated_vcf = "LCL6.high.confidence.calls.annotated.vcf"
+		File LCL7_annotated_vcf = "LCL7.high.confidence.calls.annotated.vcf"
+		File LCL8_annotated_vcf = "LCL8.high.confidence.calls.annotated.vcf"
+
+	}
+}
+
+
+
+
+
+
+