indel and snv

codescripts/vcf2bed.py

@@ -0,0 +1,42 @@
+import sys,getopt
+import os
+import fileinput
+outFile = open(sys.argv[2],'w')
+for line in fileinput.input(sys.argv[1]):
+	line = line.rstrip()
+	strings = line.strip().split('\t')
+#d5
+	if ',' in strings[6]:
+		alt_strings = strings[6].split(',')
+		alt_len = [len(i) for i in alt_strings]
+		alt = max(alt_len)
+	else:
+		alt = len(strings[6])
+	ref = strings[5]
+	pos = int(strings[1])
+	if len(ref) == 1 and alt == 1:
+		StartPos = int(pos) -1
+		EndPos = int(pos)
+		cate = 'SNV'
+	elif len(ref) > alt:
+		StartPos = int(pos) - 1
+		EndPos = int(pos) + (len(ref) - 1)
+		cate = 'INDEL'
+	elif alt > len(ref):
+		StartPos = int(pos) - 1
+		EndPos = int(pos) + (alt - 1)
+		cate = 'INDEL'
+	elif len(ref) == alt:
+		StartPos = int(pos) - 1
+		EndPos = int(pos) + (alt - 1)
+		cate = 'INDEL'
+	outline = '\t'.join(strings) + '\t' + str(StartPos) + '\t' + str(EndPos) + '\t' + cate + '\n'
+	outFile.write(outline)
+
+
+
+
+
+
+
+

inputs

@@ -1,6 +1,7 @@
 {
   "{{ project_name }}.right_200": "oss://pgx-result/renluyao/manuscript/small_variants_near_SV/chr6.ins.right.200",
   "{{ project_name }}.left_100": "oss://pgx-result/renluyao/manuscript/small_variants_near_SV/chr6.ins.left.100",
+  "{{ project_name }}.MIEpos2bed.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.4",
   "{{ project_name }}.disk_size": "100",
   "{{ project_name }}.right_50": "oss://pgx-result/renluyao/manuscript/small_variants_near_SV/chr6.ins.right.50",
   "{{ project_name }}.chromo": "chr6",
@@ -8,8 +9,8 @@
   "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
   "{{ project_name }}.right_100": "oss://pgx-result/renluyao/manuscript/small_variants_near_SV/chr6.ins.right.100",
   "{{ project_name }}.left_150": "oss://pgx-result/renluyao/manuscript/small_variants_near_SV/chr6.ins.left.150",
-  "{{ project_name }}.docker": "registry-internal.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
   "{{ project_name }}.left_200": "oss://pgx-result/renluyao/manuscript/small_variants_near_SV/chr6.ins.left.200",
+  "{{ project_name }}.bedCoverage.docker": "registry-internal.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
   "{{ project_name }}.left_50": "oss://pgx-result/renluyao/manuscript/small_variants_near_SV/chr6.ins.left.50",
   "{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc"
 }

tasks/MIEpos2bed.wdl

@@ -8,9 +8,11 @@ task MIEpos2bed {
 	
 	command <<<
 
-		cat ${mie_file} | awk '{print $1"\t"$2"\t"$2}' > ${sample_name}.${chromo}.allvariants.bed	
+		python /opt/vcf2bed.py ${mie_file} ${sample_name}.${chromo}.info.txt
 
-		cat ${mie_file} | grep -v '1:1:1' | awk '{print $1"\t"$2"\t"$2}' > ${sample_name}.${chromo}.mie.bed			
+		cat ${mie_file} | awk '{ if ($3 == 0) { print } }' | cut -f1,8,9 > ${sample_name}.${chromo}.allvariants.bed	
+
+		cat ${mie_file} | awk '{ if ($3 == 0) { print } }' | grep 'MIE' | cut -f1,8,9 > ${sample_name}.${chromo}.mie.bed			
 
 	>>>
 
@@ -21,6 +23,7 @@ task MIEpos2bed {
 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
+		File info = "${sample_name}.${chromo}.info.txt"
 		File mie_bed = "${sample_name}.${chromo}.mie.bed"
 		File all_bed = "${sample_name}.${chromo}.allvariants.bed"
 	}

workflow.wdl

@@ -13,7 +13,6 @@ workflow {{ project_name }} {
 	File right_150
 	File right_200
 	String chromo
-	String docker
 	String cluster_config
 	String disk_size
 
@@ -23,7 +22,6 @@ workflow {{ project_name }} {
 			mie_file=sample[0],
 			chromo=chromo,
 			sample_name=sample[1],
-			docker=docker,
 			cluster_config=cluster_config,
 			disk_size=disk_size
 		}
@@ -41,7 +39,6 @@ workflow {{ project_name }} {
 			right_200=right_200,
 			sample_name=sample[1],
 			chromo=chromo,
-			docker=docker,
 			cluster_config=cluster_config,
 			disk_size=disk_size
 		}