improve

codescripts/get_sv_region.sh

+cat tier1.sv tier2.sv | grep DEL | cut -f1,2,5 | sed s'/END=//g' > SV.DEL
+cat tier1.sv tier2.sv | grep DUP | cut -f1,2,5 | sed s'/END=//g' > SV.DUP
+
+cat tier1.sv tier2.sv | grep INS | cut -f1,2 > SV.INS
+cat SV.INS | awk '{print $1 "\t" ($2 - 500) "\t" ($2+500)}' | sort -k1,1 -k2,2n > sv.ins.break.point.500.bed
+
+cat SV.DEL | awk '{print $1 "\t" ($2 - 500) "\t" $2}'  > sv.del.break.point.left
+cat SV.DEL | awk '{print $1 "\t" $3 "\t" ($3 + 500)}'  > sv.del.break.point.right
+cat sv.del.break.point.left sv.del.break.point.right | sort -k1,1 -k2,2n > sv.del.break.point.500.bed
+
+cat tier1.sv tier2.sv | grep TRA | grep -v 'chrM' | cut -f1,2,4,5  > SV.TRA
+cat SV.TRA | awk '{print $1 "\t" ($2 - 500) "\t" ($2 + 500)}' > sv.tra.chr1
+cat SV.TRA | cut -f3,4 | sed s'/CHR2=//g' | sed s'/END=//g' |awk '{print $1 "\t" ($2 - 500) "\t" ($2 + 500)}' > sv.tra.chr2
+cat sv.tra.chr1 sv.tra.chr2 | sort -k1,1 -k2,2n > sv.tra.break.point.500.bed
+
+cat tier1.sv tier2.sv | grep INV | cut -f1,2,5 | sed s'/END=//g' > SV.INV
+cat SV.INV | awk '{print $1 "\t" ($2 - 500) "\t" $2}'  > sv.inv.break.point.left
+cat SV.INV | awk '{print $1 "\t" $3 "\t" ($3 + 500)}'  > sv.inv.break.point.right
+cat sv.inv.break.point.left sv.inv.break.point.right | sort -k1,1 -k2,2n > sv.inv.break.point.500.bed
+
+cat SV.DUP | awk '{print $1 "\t" ($2 - 500) "\t" $2}'  > sv.dup.break.point.left
+cat SV.DUP | awk '{print $1 "\t" $3 "\t" ($3 + 500)}'  > sv.dup.break.point.right
+cat sv.dup.break.point.left sv.dup.break.point.right | grep -v 'chrM' | sort -k1,1 -k2,2n > sv.dup.break.point.500.bed
+
+
+cat SV.INS | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.50
+cat sv.ins.left.50 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.100
+cat sv.ins.left.100 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.150
+cat sv.ins.left.150 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.200
+cat sv.ins.left.200 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.250
+cat sv.ins.left.250 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.300
+cat sv.ins.left.300 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.350
+cat sv.ins.left.350 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.400
+
+
+cat SV.INS | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.50
+cat sv.ins.right.50 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.100
+cat sv.ins.right.100 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.150
+cat sv.ins.right.150 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.200
+cat sv.ins.right.200 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.250
+cat sv.ins.right.250 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.300
+cat sv.ins.right.300 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.350
+cat sv.ins.right.350 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.400
+
+
+
+cat SV.INS | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.50
+cat sv.ins.left.50 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.100
+cat sv.ins.left.100 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.150
+cat sv.ins.left.150 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.200
+cat sv.ins.left.200 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.250
+cat sv.ins.left.250 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.300
+cat sv.ins.left.300 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.350
+cat sv.ins.left.350 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.400
+
+
+cat SV.INS | awk '{print $1"\t"$2 "\t" ($2 + 50)}' > sv.ins.right.50
+cat sv.ins.right.50 | awk '{print $1"\t"$2 "\t" ($2 + 50)}' > sv.ins.right.100
+cat sv.ins.right.100 | awk '{print $1"\t"$2 "\t" ($2 + 50)}' > sv.ins.right.150
+cat sv.ins.right.150 | awk '{print $1"\t"$2 "\t" ($2 + 50)}' > sv.ins.right.200
+cat sv.ins.right.200 | awk '{print $1"\t"$2 "\t" ($2 + 50)}' > sv.ins.right.250
+cat sv.ins.right.250 | awk '{print $1"\t"$2 "\t" ($2 + 50)}' > sv.ins.right.300
+cat sv.ins.right.300 | awk '{print $1"\t"$2 "\t" ($2 + 50)}' > sv.ins.right.350
+cat sv.ins.right.350 | awk '{print $1"\t"$2 "\t" ($2 + 50)}' > sv.ins.right.400
+
+
+
+cat SV.DEL | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.50
+cat sv.del.left.50 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.100
+cat sv.del.left.100 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.150
+cat sv.del.left.150 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.200
+cat sv.del.left.200 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.250
+cat sv.del.left.250 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.300
+cat sv.del.left.300 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.350
+cat sv.del.left.350 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.400
+
+
+cat SV.DEL | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.50
+cat sv.del.right.50 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.100
+cat sv.del.right.100 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.150
+cat sv.del.right.150 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.200
+cat sv.del.right.200 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.250
+cat sv.del.right.250 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.300
+cat sv.del.right.300 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.350
+cat sv.del.right.350 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.400
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 

inputs

 {
-  "{{ 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 }}.INS_bedAnnotation.right_150": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.right.150",
+  "{{ project_name }}.INS_bedAnnotation.left_400": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.left.400",
+  "{{ project_name }}.INS_bedCoverage.right_200": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.right.200",
+  "{{ project_name }}.INS_bedCoverage.right_100": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.right.100",
+  "{{ project_name }}.INS_bedAnnotation.left_350": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.left.350",
+  "{{ project_name }}.INS_bedAnnotation.right_200": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.right.200",
   "{{ project_name }}.MIEpos2bed.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.4",
+  "{{ project_name }}.INS_bedCoverage.docker": "registry-internal.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
+  "{{ project_name }}.diffBed.docker": "registry-internal.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
+  "{{ project_name }}.INS_bedCoverage.left_400": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.left.400",
+  "{{ project_name }}.INS_bedAnnotation.left_300": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.left.300",
+  "{{ project_name }}.INS_bedCoverage.right_400": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.right.400",
   "{{ 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",
-  "{{ project_name }}.right_150": "oss://pgx-result/renluyao/manuscript/small_variants_near_SV/chr6.ins.right.150",
+  "{{ project_name }}.DEL_bedCoverage.right_150": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/DEL_break_points/sv.del.right.150",
+  "{{ project_name }}.DEL_bedCoverage.left_400": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/DEL_break_points/sv.del.left.400",
+  "{{ project_name }}.DEL_bedCoverage.left_200": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/DEL_break_points/sv.del.left.200",
+  "{{ project_name }}.INS_bedAnnotation.left_200": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.left.200",
+  "{{ project_name }}.INS_bedCoverage.right_50": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.right.50",
+  "{{ project_name }}.INS_bedAnnotation.right_300": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.right.300",
+  "{{ project_name }}.INS_bedAnnotation.right_350": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.right.350",
   "{{ 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 }}.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"
+  "{{ project_name }}.DEL_bedCoverage.left_350": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/DEL_break_points/sv.del.left.350",
+  "{{ project_name }}.diffBed.centromere": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/centro_pericentro_region.bed",
+  "{{ project_name }}.diffBed.sv_tra_bp": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/sv.tra.break.point.500.bed",
+  "{{ project_name }}.diffBed.sv_del": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/SV.DEL",
+  "{{ project_name }}.INS_bedAnnotation.right_50": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.right.50",
+  "{{ project_name }}.sample_name": "{{ sample_name }}",
+  "{{ project_name }}.DEL_bedCoverage.right_200": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/DEL_break_points/sv.del.right.200",
+  "{{ project_name }}.INS_bedCoverage.left_250": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.left.250",
+  "{{ project_name }}.INS_bedCoverage.left_150": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.left.150",
+  "{{ project_name }}.INS_bedAnnotation.left_150": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.left.150",
+  "{{ project_name }}.INS_bedAnnotation.right_400": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.right.400",
+  "{{ project_name }}.INS_bedCoverage.right_150": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.right.150",
+  "{{ project_name }}.DEL_bedCoverage.right_250": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/DEL_break_points/sv.del.right.250",
+  "{{ project_name }}.DEL_bedCoverage.right_300": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/DEL_break_points/sv.del.right.300",
+  "{{ project_name }}.diffBed.sv_ins_bp": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/sv.ins.break.point.500.bed",
+  "{{ project_name }}.diffBed.sv_inv": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/SV.INV",
+  "{{ project_name }}.INS_bedCoverage.left_350": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.left.350",
+  "{{ project_name }}.INS_bedAnnotation.right_250": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.right.250",
+  "{{ project_name }}.DEL_bedCoverage.left_100": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/DEL_break_points/sv.del.left.100",
+  "{{ project_name }}.DEL_bedCoverage.left_250": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/DEL_break_points/sv.del.left.250",
+  "{{ project_name }}.INS_bedCoverage.left_300": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.left.300",
+  "{{ project_name }}.DEL_bedCoverage.right_100": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/DEL_break_points/sv.del.right.100",
+  "{{ project_name }}.INS_bedAnnotation.left_250": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.left.250",
+  "{{ project_name }}.diffBed.lcr": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/btu356_LCR-hs38.bed",
+  "{{ project_name }}.INS_bedCoverage.left_50": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.left.50",
+  "{{ project_name }}.DEL_bedCoverage.left_50": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/DEL_break_points/sv.del.left.50",
+  "{{ project_name }}.INS_bedCoverage.right_300": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.right.300",
+  "{{ project_name }}.INS_bedCoverage.right_250": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.right.250",
+  "{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc",
+  "{{ project_name }}.INS_bedAnnotation.left_100": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.left.100",
+  "{{ project_name }}.mergeBed.docker": "registry-internal.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
+  "{{ project_name }}.diffBed.sv_dup_bp": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/sv.dup.break.point.500.bed",
+  "{{ project_name }}.DEL_bedCoverage.docker": "registry-internal.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
+  "{{ project_name }}.diffBed.sv_del_bp": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/sv.del.break.point.500.bed",
+  "{{ project_name }}.DEL_bedCoverage.left_150": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/DEL_break_points/sv.del.left.50",
+  "{{ project_name }}.INS_bedCoverage.right_350": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.right.350",
+  "{{ project_name }}.DEL_bedCoverage.right_350": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/DEL_break_points/sv.del.right.350",
+  "{{ project_name }}.INS_bedCoverage.left_200": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.left.200",
+  "{{ project_name }}.DEL_bedCoverage.right_400": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/DEL_break_points/sv.del.right.400",
+  "{{ project_name }}.INS_bedCoverage.left_100": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.left.100",
+  "{{ project_name }}.diffBed.sv_dup": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/SV.DUP",
+  "{{ project_name }}.INS_bedAnnotation.docker": "registry-internal.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
+  "{{ project_name }}.diffBed.easy_region": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/easy_region.bed",
+  "{{ project_name }}.diffBed.sv_inv_bp": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/sv.inv.break.point.500.bed",
+  "{{ project_name }}.INS_bedAnnotation.right_100": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.right.100",
+  "{{ project_name }}.DEL_bedCoverage.left_300": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/DEL_break_points/sv.del.left.300",
+  "{{ project_name }}.INS_bedAnnotation.left_50": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/INS_break_points/sv.ins.left.50",
+  "{{ project_name }}.DEL_bedCoverage.right_50": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/DEL_break_points/sv.del.right.50"
 }

tasks/MIEpos2bed.wdl

 
 		cat ${sample_name}.${chromo}.info.txt | grep -v '0:4:4' | grep -v '1:4:4' | awk '{ if ($3 != 0) { print } }' | cut -f1,8,9 > ${sample_name}.${chromo}.allvariants.bed	
 
-		cat ${sample_name}.${chromo}.info.txt | grep -v '0:4:4' | grep -v '1:4:4' | awk '{ if ($3 != 0) { print } }' | grep 'MIE' | cut -f1,8,9 > ${sample_name}.${chromo}.mie.bed			
+		cat ${sample_name}.${chromo}.info.txt | grep -v '0:4:4' | grep -v '1:4:4' | awk '{ if ($3 != 0) { print } }' | grep 'MIE' | cut -f1,8,9 > ${sample_name}.${chromo}.mie.bed
+
+		cat ${sample_name}.${chromo}.info.txt | awk '{print $1,$8,$9,$10,$2,$3,$4,$5,$6,$7}' | sed 's/\s\+/\t/g' > ${sample_name}.${chromo}.info.bed
 
 	>>>
 
 		File info = "${sample_name}.${chromo}.info.txt"
 		File mie_bed = "${sample_name}.${chromo}.mie.bed"
 		File all_bed = "${sample_name}.${chromo}.allvariants.bed"
+		File info_bed = "${sample_name}.${chromo}.info.bed"
 	}
 }

tasks/bedAnnotation.wdl

+task bedAnnotation {
+	File all_info_bed
+	File left_50
+	File left_100
+	File left_150
+	File left_200
+	File left_250
+	File left_300
+	File left_350
+	File left_400
+	File right_50
+	File right_100
+	File right_150
+	File right_200
+	File right_250
+	File right_300
+	File right_350
+	File right_400
+	String sample_name
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${all_info_bed} -files ${left_400} ${left_350} ${left_300} ${left_250} ${left_200} ${left_150} ${left_100} ${left_50} ${right_50} ${right_100} ${right_150} ${right_200} ${right_250} ${right_300} ${right_350} ${right_400} > ${sample_name}.info.bed.annotation.txt
+
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File info_bed_annotation = "${sample_name}.info.bed.annotation.txt"
+	}
+}

tasks/bedCoverage.wdl

 task bedCoverage {
-	File mie_bed
-	File all_bed
+	File all_mie_bed
+	File all_all_bed
 	File left_50
 	File left_100
 	File left_150
 	File left_200
+	File left_250
+	File left_300
+	File left_350
+	File left_400
 	File right_50
 	File right_100
 	File right_150
 	File right_200
+	File right_250
+	File right_300
+	File right_350
+	File right_400
 	String sample_name
-	String chromo
 	String docker
 	String cluster_config
 	String disk_size
 	command <<<
 
 ## MIE
-		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_50} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.left50.coverage.txt
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_50} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.left50.coverage.txt
 
-		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_100} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.left100.coverage.txt
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_100} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.left100.coverage.txt
 
-		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_150} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.left150.coverage.txt
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_150} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.left150.coverage.txt
 
-		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_200} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.left200.coverage.txt
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_200} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.left200.coverage.txt
 
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_250} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.left250.coverage.txt
 
-		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_50} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.right50.coverage.txt
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_300} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.left300.coverage.txt
 
-		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_100} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.right100.coverage.txt
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_350} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.left350.coverage.txt
 
-		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_150} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.right150.coverage.txt
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_400} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.left400.coverage.txt
 
-		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_200} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.right200.coverage.txt
 
-		paste ${sample_name}.${chromo}.mie.left200.coverage.txt ${sample_name}.${chromo}.mie.left150.coverage.txt ${sample_name}.${chromo}.mie.left100.coverage.txt ${sample_name}.${chromo}.mie.left50.coverage.txt ${sample_name}.${chromo}.mie.right50.coverage.txt ${sample_name}.${chromo}.mie.right100.coverage.txt ${sample_name}.${chromo}.mie.right150.coverage.txt ${sample_name}.${chromo}.mie.right200.coverage.txt > ${sample_name}.${chromo}.mie.coverage.txt
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_50} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.right50.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_100} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.right100.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_150} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.right150.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_200} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.right200.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_250} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.right250.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_300} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.right300.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_350} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.right350.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_400} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.right400.coverage.txt
+
+
+		paste ${sample_name}.mie.left400.coverage.txt ${sample_name}.mie.left350.coverage.txt ${sample_name}.mie.left300.coverage.txt ${sample_name}.mie.left250.coverage.txt ${sample_name}.mie.left200.coverage.txt ${sample_name}.mie.left150.coverage.txt ${sample_name}.mie.left100.coverage.txt ${sample_name}.mie.left50.coverage.txt ${sample_name}.mie.right50.coverage.txt ${sample_name}.mie.right100.coverage.txt ${sample_name}.mie.right150.coverage.txt ${sample_name}.mie.right200.coverage.txt ${sample_name}.mie.right250.coverage.txt ${sample_name}.mie.right300.coverage.txt ${sample_name}.mie.right350.coverage.txt ${sample_name}.mie.right400.coverage.txt > ${sample_name}.mie.coverage.txt
 
 # all variants
 
-		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_50} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.left50.coverage.txt
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_50} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.left50.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_100} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.left100.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_150} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.left150.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_200} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.left200.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_250} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.left250.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_300} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.left300.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_350} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.left350.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_400} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.left400.coverage.txt
+
 
-		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_100} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.left100.coverage.txt
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_50} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.right50.coverage.txt
 
-		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_150} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.left150.coverage.txt
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_100} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.right100.coverage.txt
 
-		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_200} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.left200.coverage.txt
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_150} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.right150.coverage.txt
 
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_200} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.right200.coverage.txt
 
-		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_50} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.right50.coverage.txt
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_250} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.right250.coverage.txt
 
-		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_100} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.right100.coverage.txt
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_300} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.right300.coverage.txt
 
-		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_150} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.right150.coverage.txt
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_350} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.right350.coverage.txt
 
-		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_200} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.right200.coverage.txt
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_400} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.right400.coverage.txt
 
-		paste ${sample_name}.${chromo}.all.left200.coverage.txt ${sample_name}.${chromo}.all.left150.coverage.txt ${sample_name}.${chromo}.all.left100.coverage.txt ${sample_name}.${chromo}.all.left50.coverage.txt ${sample_name}.${chromo}.all.right50.coverage.txt ${sample_name}.${chromo}.all.right100.coverage.txt ${sample_name}.${chromo}.all.right150.coverage.txt ${sample_name}.${chromo}.all.right200.coverage.txt > ${sample_name}.${chromo}.all.coverage.txt
 
+		paste ${sample_name}.all.left400.coverage.txt ${sample_name}.all.left350.coverage.txt ${sample_name}.all.left300.coverage.txt ${sample_name}.all.left250.coverage.txt ${sample_name}.all.left200.coverage.txt ${sample_name}.all.left150.coverage.txt ${sample_name}.all.left100.coverage.txt ${sample_name}.all.left50.coverage.txt ${sample_name}.all.right50.coverage.txt ${sample_name}.all.right100.coverage.txt ${sample_name}.all.right150.coverage.txt ${sample_name}.all.right200.coverage.txt ${sample_name}.all.right250.coverage.txt ${sample_name}.all.right300.coverage.txt ${sample_name}.all.right350.coverage.txt ${sample_name}.all.right400.coverage.txt > ${sample_name}.all.coverage.txt
 
 	>>>
 
 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File mie = "${sample_name}.${chromo}.mie.coverage.txt"
-		File all = "${sample_name}.${chromo}.all.coverage.txt"
+		File mie = "${sample_name}.mie.coverage.txt"
+		File all = "${sample_name}.all.coverage.txt"
 	}
 }

tasks/diffBed.wdl

+task diffBed {
+	File all_mie_bed
+	File all_all_bed
+	File lcr
+	File centromere
+	File sv_dup
+	File sv_del
+	File sv_inv
+	File easy_region
+	File sv_ins_bp
+	File sv_del_bp
+	File sv_tra_bp
+	File sv_inv_bp
+	File sv_dup_bp
+	String sample_name
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+
+# mie
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${lcr} -b ${all_mie_bed} -counts  > ${sample_name}.mie.lcr.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${centromere} -b ${all_mie_bed} -counts  > ${sample_name}.mie.centromere.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_dup} -b ${all_mie_bed} -counts  > ${sample_name}.mie.sv_dup.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_del} -b ${all_mie_bed} -counts  > ${sample_name}.mie.sv_del.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_inv} -b ${all_mie_bed} -counts  > ${sample_name}.mie.sv_inv.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_ins_bp} -b ${all_mie_bed} -counts  > ${sample_name}.mie.sv_ins_bp.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_del_bp} -b ${all_mie_bed} -counts  > ${sample_name}.mie.sv_del_bp.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_tra_bp} -b ${all_mie_bed} -counts  > ${sample_name}.mie.sv_tra_bp.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_inv_bp} -b ${all_mie_bed} -counts  > ${sample_name}.mie.sv_inv_bp.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_dup_bp} -b ${all_mie_bed} -counts  > ${sample_name}.mie.sv_dup_bp.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${easy_region} -b ${all_mie_bed} -counts  > ${sample_name}.mie.easy_region.coverage.txt
+
+
+# all variants
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${lcr} -b ${all_all_bed} -counts  > ${sample_name}.all.lcr.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${centromere} -b ${all_all_bed} -counts  > ${sample_name}.all.centromere.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_dup} -b ${all_all_bed} -counts  > ${sample_name}.all.sv_dup.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_del} -b ${all_all_bed} -counts  > ${sample_name}.all.sv_del.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_inv} -b ${all_all_bed} -counts  > ${sample_name}.all.sv_inv.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_ins_bp} -b ${all_all_bed} -counts  > ${sample_name}.all.sv_ins_bp.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_del_bp} -b ${all_all_bed} -counts  > ${sample_name}.all.sv_del_bp.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_tra_bp} -b ${all_all_bed} -counts  > ${sample_name}.all.sv_tra_bp.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_inv_bp} -b ${all_all_bed} -counts  > ${sample_name}.all.sv_inv_bp.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_dup_bp} -b ${all_all_bed} -counts  > ${sample_name}.all.sv_dup_bp.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${easy_region} -b ${all_all_bed} -counts  > ${sample_name}.all.easy_region.coverage.txt
+
+
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File mie_lcr = "${sample_name}.mie.lcr.coverage.txt"
+		File mie_centromere = "${sample_name}.mie.centromere.coverage.txt"
+		File mie_sv_dup = "${sample_name}.mie.sv_dup.coverage.txt"
+		File mie_sv_del = "${sample_name}.mie.sv_del.coverage.txt"
+		File mie_sv_inv = "${sample_name}.mie.sv_inv.coverage.txt"
+		File mie_sv_ins_bp = "${sample_name}.mie.sv_ins_bp.coverage.txt"
+		File mie_sv_del_bp = "${sample_name}.mie.sv_del_bp.coverage.txt"
+		File mie_sv_tra_bp = "${sample_name}.mie.sv_tra_bp.coverage.txt"
+		File mie_sv_inv_bp = "${sample_name}.mie.sv_inv_bp.coverage.txt"
+		File mie_sv_dup_bp = "${sample_name}.mie.sv_dup_bp.coverage.txt"
+		File mie_easy_region = "${sample_name}.mie.easy_region.coverage.txt"
+		File all_lcr = "${sample_name}.all.lcr.coverage.txt"
+		File all_centromere = "${sample_name}.all.centromere.coverage.txt"
+		File all_sv_dup = "${sample_name}.all.sv_dup.coverage.txt"
+		File all_sv_del = "${sample_name}.all.sv_del.coverage.txt"
+		File all_sv_inv = "${sample_name}.all.sv_inv.coverage.txt"
+		File all_sv_ins_bp = "${sample_name}.all.sv_ins_bp.coverage.txt"
+		File all_sv_del_bp = "${sample_name}.all.sv_del_bp.coverage.txt"
+		File all_sv_tra_bp = "${sample_name}.all.sv_tra_bp.coverage.txt"
+		File all_sv_inv_bp = "${sample_name}.all.sv_inv_bp.coverage.txt"
+		File all_sv_dup_bp = "${sample_name}.all.sv_dup_bp.coverage.txt"
+		File all_easy_region = "${sample_name}.all.easy_region.coverage.txt"
+	}
+}

tasks/mergeBed.wdl

+task mergeBed {
+	Array[File] mie_bed
+	Array[File] all_bed
+	Array[File] info_bed
+	String sample_name
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+
+		cat ${sep=" " mie_bed} > ${sample_name}.mie.bed
+
+		cat ${sep=" " all_bed} > ${sample_name}.all.bed
+
+		cat ${sep=" " info_bed} > ${sample_name}.info.bed
+
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File all_mie_bed = "${sample_name}.mie.bed"
+		File all_all_bed = "${sample_name}.all.bed"
+		File all_info_bed = "${sample_name}.info.bed"
+	}
+}

workflow.wdl

 import "./tasks/MIEpos2bed.wdl" as MIEpos2bed
+import "./tasks/mergeBed.wdl" as mergeBed
 import "./tasks/bedCoverage.wdl" as bedCoverage
+import "./tasks/diffBed.wdl" as diffBed
+import "./tasks/bedAnnotation.wdl" as bedAnnotation
 
 workflow {{ project_name }} {
 	File inputSamplesFile
 	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
-	File left_50
-	File left_100
-	File left_150
-	File left_200
-	File right_50
-	File right_100
-	File right_150
-	File right_200
-	String chromo
+	String sample_name
 	String cluster_config
 	String disk_size
 
 		call MIEpos2bed.MIEpos2bed as MIEpos2bed {
 			input:
 			mie_file=sample[0],
-			chromo=chromo,
-			sample_name=sample[1],
-			cluster_config=cluster_config,
-			disk_size=disk_size
-		}
-		call bedCoverage.bedCoverage as bedCoverage {
-			input:
-			mie_bed=MIEpos2bed.mie_bed,
-			all_bed=MIEpos2bed.all_bed,
-			left_50=left_50,
-			left_100=left_100,
-			left_150=left_150,
-			left_200=left_200,
-			right_50=right_50,
-			right_100=right_100,
-			right_150=right_150,
-			right_200=right_200,
-			sample_name=sample[1],
-			chromo=chromo,
+			chromo=sample[1],
+			sample_name=sample_name,
 			cluster_config=cluster_config,
 			disk_size=disk_size
 		}
 	}
+	call mergeBed.mergeBed as mergeBed {
+		input:
+		mie_bed=MIEpos2bed.mie_bed,
+		all_bed=MIEpos2bed.all_bed,
+		info_bed=MIEpos2bed.info_bed,
+		sample_name=sample_name,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+	call bedCoverage.bedCoverage as INS_bedCoverage {
+		input:
+		all_mie_bed=mergeBed.all_mie_bed,
+		all_all_bed=mergeBed.all_all_bed,
+		sample_name=sample_name,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+	call bedCoverage.bedCoverage as DEL_bedCoverage {
+		input:
+		all_mie_bed=mergeBed.all_mie_bed,
+		all_all_bed=mergeBed.all_all_bed,
+		sample_name=sample_name,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+	call diffBed.diffBed as diffBed {
+		input:
+		all_mie_bed=mergeBed.all_mie_bed,
+		all_all_bed=mergeBed.all_all_bed,
+		sample_name=sample_name,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+	call bedAnnotation.bedAnnotation as INS_bedAnnotation {
+		input:
+		all_info_bed=mergeBed.all_info_bed,
+		sample_name=sample_name,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
 }