feat: qc and multi callers

defaults

@@ -21,7 +21,10 @@
   "germline_resource_tbi": "oss://genomics-platform-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz.tbi",
   "gc": "oss://ivd-product/reference/Sequenza/GRCh38.gc50Base.wig.gz",
   "baseline": "oss://ivd-product/reference/MSIsensor/hg38_reference.list_baseline",
+  "fastq_screen_conf": "oss://genomics-platform-reference-data/fastq_screen_reference/fastq_screen.conf",
+  "screen_ref_dir": "oss://genomics-platform-reference-data/fastq_screen_reference/",
   "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/sentieon-genomics:v202112.05",
+  "varscan_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/varscan2:v2.4.3",
   "manta_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/manta:1.6.0",
   "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/bcftools:v1.9",
   "annovar_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/annovar:v20191024",
@@ -29,8 +32,13 @@
   "cnvkit_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/cnvkit:0.9.9",
   "sequenza_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/sequenza:3.0.0",
   "msisensor_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/msisensor-pro:1.2.0",
+  "fastqscreen_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/fastqscreen:0.12.0",
+  "fastqc_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/fastqc:0.11.8",
+  "qualimap_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/qualimap:2.0.0",
   "tmb_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/tmb:1.0.0",
   "cluster_16cpu_32gb": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
   "cluster_2cpu_4gb": "OnDemand bcs.es.c.large img-ubuntu-vpc",
-  "disk_size": "500"
+  "disk_size": "500",
+  "qc": false,
+  "multi_caller": false
 }

inputs

@@ -8,6 +8,7 @@
   "{{ project_name }}.duplex_umi": "{{ duplex_umi }}",
   "{{ project_name }}.SENTIEON_LICENSE": "{{ SENTIEON_LICENSE }}",
   "{{ project_name }}.sentieon_docker": "{{ sentieon_docker }}",
+  "{{ project_name }}.varscan_docker": "{{ varscan_docker }}",
   "{{ project_name }}.manta_docker": "{{ manta_docker }}",
   "{{ project_name }}.bcftools_docker": "{{ bcftools_docker }}",
   "{{ project_name }}.annovar_docker": "{{ annovar_docker }}",
@@ -16,6 +17,11 @@
   "{{ project_name }}.sequenza_docker": "{{ sequenza_docker }}",
   "{{ project_name }}.msisensor_docker": "{{ msisensor_docker }}",
   "{{ project_name }}.tmb_docker": "{{ tmb_docker }}",
+  "{{ project_name }}.fastqscreen_docker": "{{ fastqscreen_docker }}",
+  "{{ project_name }}.fastqc_docker": "{{ fastqc_docker }}",
+  "{{ project_name }}.qualimap_docker": "{{ qualimap_docker }}",
+  "{{ project_name }}.fastq_screen_conf": "{{ fastq_screen_conf }}",
+  "{{ project_name }}.screen_ref_dir": "{{ screen_ref_dir }}",
   "{{ project_name }}.platform": "{{ platform }}",
   "{{ project_name }}.fasta": "{{ fasta }}",
   "{{ project_name }}.ref_dir": "{{ ref_dir }}",
@@ -34,5 +40,7 @@
   "{{ project_name }}.ref_flat": "{{ ref_flat }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_2cpu_4gb": "{{ cluster_2cpu_4gb }}",
-  "{{ project_name }}.cluster_16cpu_32gb": "{{ cluster_16cpu_32gb }}"
+  "{{ project_name }}.cluster_16cpu_32gb": "{{ cluster_16cpu_32gb }}",
+  "{{ project_name }}.qc": {{ qc | tojson }},
+  "{{ project_name }}.multi_caller": {{ multi_caller | tojson }}
 }

tasks/TNscope.wdl

@@ -0,0 +1,73 @@
+task TNscope {
+  
+  String sample
+  String SENTIEON_LICENSE
+  File tumor_recaled_bam
+  File tumor_recaled_bam_index
+  File? normal_recaled_bam
+  File? normal_recaled_bam_index
+  String tumor_name
+  String normal_name
+
+  File ref_dir
+  String fasta
+  File dbsnp_dir
+  String dbsnp
+  File? regions
+  Int? interval_padding
+  File? pon_vcf
+
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+    nt=$(nproc)
+    
+    if [ ${regions} ]; then
+      INTERVAL="--interval ${regions} --interval_padding ${interval_padding}"
+    else
+      INTERVAL=""
+    fi
+    
+    # if [ ${pon_vcf} ]; then
+    #   PON="--pon ${pon_vcf}"
+    #   sentieon util vcfindex ${pon_vcf}
+    # else
+    #   PON=""
+    # fi
+    
+    if [ ${normal_recaled_bam} ]; then
+      INPUT="-i ${tumor_recaled_bam} -i ${normal_recaled_bam}"
+      SAMPLE="--tumor_sample ${tumor_name} --normal_sample ${normal_name}"
+    else
+      INPUT="-i ${tumor_recaled_bam}"
+      SAMPLE="--tumor_sample ${tumor_name}"
+    fi
+    
+    sentieon driver -t $nt -r ${ref_dir}/${fasta} \
+    $INPUT \
+    $INTERVAL \
+    --algo TNscope \
+    $SAMPLE \
+    --dbsnp ${dbsnp_dir}/${dbsnp} \
+    ${sample}.TNscope.vcf
+    
+    # awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${sample}.TNscope.vcf > ${sample}.TNscope.PASS.vcf
+  >>>
+
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+
+  output {
+    File TNscope_vcf= "${sample}.TNscope.vcf"
+    File TNscope_vcf_index = "${sample}.TNscope.vcf.idx"
+  }
+}

tasks/fastqc.wdl

@@ -0,0 +1,33 @@
+task fastqc {
+  
+  String sample
+  File read1
+  File read2
+  
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    ln -s ${read1} ${sample}_R1.fastq.gz
+    ln -s ${read2} ${sample}_R2.fastq.gz
+    fastqc -t $nt -o ./ ${sample}_R1.fastq.gz
+    fastqc -t $nt -o ./ ${sample}_R2.fastq.gz
+  >>>
+
+  runtime {
+    docker:docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  output {
+    File read1_html="${sample}_R1_fastqc.html"
+    File read1_zip="${sample}_R1_fastqc.zip"
+    File read2_html="${sample}_R2_fastqc.html"
+    File read2_zip="${sample}_R2_fastqc.zip"
+  }
+}

tasks/fastqscreen.wdl

@@ -0,0 +1,40 @@
+task fastq_screen {
+  
+  String sample
+  File read1
+  File read2
+  File screen_ref_dir
+  File fastq_screen_conf
+
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    mkdir -p /cromwell_root/tmp
+    cp -r ${screen_ref_dir} /cromwell_root/tmp/
+    ln -s ${read1} ${sample}_R1.fastq.gz
+    ln -s ${read2} ${sample}_R2.fastq.gz
+    fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${sample}_R1.fastq.gz
+    fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${sample}_R2.fastq.gz
+  >>>
+
+  runtime {
+    docker:docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+
+  output {
+    File png1 = "${sample}_R1_screen.png"
+    File txt1 = "${sample}_R1_screen.txt"
+    File html1 = "${sample}_R1_screen.html"
+    File png2 = "${sample}_R2_screen.png"
+    File txt2 = "${sample}_R2_screen.txt"
+    File html2 = "${sample}_R2_screen.html"
+  }
+}

tasks/processSomatic.wdl

@@ -0,0 +1,40 @@
+task processSomatic {
+  
+  String sample
+  File varscan_snp
+  File varscan_indel
+  
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    cp ${varscan_snp} ./
+    cp ${varscan_indel} ./
+    java -Xmx32g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.SNP.vcf
+    java -Xmx32g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.INDEL.vcf
+
+  >>>
+
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+
+  output {
+    File varscan_snp_somatic = "${sample}.VarScan.SNP.Somatic.vcf"
+    File varscan_snp_germline = "${sample}.VarScan.SNP.Germline.vcf"
+    File varscan_snp_loh = "${sample}.VarScan.SNP.LOH.vcf"
+    File varscan_snp_somatic_hc = "${sample}.VarScan.SNP.Somatic.hc.vcf"
+    File varscan_snp_germline_hc = "${sample}.VarScan.SNP.Germline.hc.vcf"
+    File varscan_snp_loh_hc = "${sample}.VarScan.SNP.LOH.hc.vcf"
+    File varscan_indel_somatic = "${sample}.VarScan.INDEL.Somatic.vcf"
+    File varscan_indel_germline = "${sample}.VarScan.INDEL.Germline.vcf"
+    File varscan_indel_loh = "${sample}.VarScan.INDEL.LOH.vcf"
+    File varscan_indel_somatic_hc = "${sample}.VarScan.INDEL.Somatic.hc.vcf"
+    File varscan_indel_germline_hc = "${sample}.VarScan.INDEL.Germline.hc.vcf"
+    File varscan_indel_loh_hc = "${sample}.VarScan.INDEL.LOH.hc.vcf"
+  }
+}

tasks/qualimap.wdl

@@ -0,0 +1,33 @@
+task qualimap {
+  
+  String sample
+  File bam
+  File bai
+  File covered_bed
+  
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    awk 'BEGIN{OFS="\t"}{sub("\r","",$3);print $1,$2,$3,"",0,"."}' ${covered_bed} > new.bed
+    /opt/qualimap/qualimap bamqc -bam ${bam} -gff new.bed -outformat PDF:HTML -nt $nt -outdir ${sample} --java-mem-size=32G
+    cat ${sample}/genome_results.txt | grep duplication | awk -F "= |%" '{print "'"${sample}"'""\t"$2}' > ${sample}_qualimap_duplication.txt
+    tar -zcvf ${sample}_qualimap.tar ${sample}
+  >>>
+
+  runtime {
+    docker:docker
+    cluster:cluster_config
+    systemDisk:"cloud_ssd 40"
+    dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File tar = "${sample}_qualimap.tar"
+    File duplication = "${sample}_qualimap_duplication.txt"
+  }
+}

tasks/somatic.wdl

@@ -0,0 +1,31 @@
+task somatic {
+
+  String sample
+  File normal_bam
+  File normal_bam_index
+  File tumor_bam
+  File tumor_bam_index
+
+  File ref_dir
+  String fasta  
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    samtools mpileup -f ${ref_dir}/${fasta} -B ${normal_bam} ${tumor_bam} | java -Xmx32g -jar /opt/VarScan.v2.4.3.jar somatic --mpileup 1 --min-coverage 3 --min-coverage-normal 3 --min-coverage-tumor 3 --min-var-freq 0.08 --p-value 0.10 --somatic-p-value 0.05 --output-vcf 1 --output-snp ${sample}.VarScan.SNP --output-indel ${sample}.VarScan.INDEL --strand-filter 1
+  >>>
+
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File varscan_snp = "${sample}.VarScan.SNP.vcf"
+    File varscan_indel = "${sample}.VarScan.INDEL.vcf"
+    
+  }
+}

tasks/somaticFilter.wdl

@@ -0,0 +1,47 @@
+task somaticFilter {
+  
+  String sample
+  File varscan_snp_somatic_hc
+  File varscan_snp_germline_hc
+  File varscan_snp_loh_hc
+  File varscan_indel_somatic_hc
+  File varscan_indel_germline_hc
+  File varscan_indel_loh_hc
+  File varscan_indel
+
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    java -Xmx32g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.SNP.Somatic.filter.vcf
+
+    java -Xmx32g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.SNP.Germline.filter.vcf
+
+    java -Xmx32g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.SNP.LOH.filter.vcf
+
+    java -Xmx32g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.INDEL.Somatic.filter.vcf
+
+    java -Xmx32g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.INDEL.Germline.filter.vcf
+
+    java -Xmx32g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.INDEL.LOH.filter.vcf
+
+    # Merge SNP and INDEL
+    awk '{if ($1!~/^#/) print}' ${sample}.VarScan.SNP.Somatic.filter.vcf | cat ${sample}.VarScan.INDEL.Somatic.filter.vcf - > ${sample}.VarScan.Somatic.filter.vcf
+    awk '{if ($1!~/^#/) print}' ${sample}.VarScan.SNP.Germline.filter.vcf | cat ${sample}.VarScan.INDEL.Germline.filter.vcf - > ${sample}.VarScan.Germline.filter.vcf
+    awk '{if ($1!~/^#/) print}' ${sample}.VarScan.SNP.LOH.filter.vcf | cat ${sample}.VarScan.INDEL.LOH.filter.vcf - > ${sample}.VarScan.LOH.filter.vcf
+  >>>
+
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+
+  output {
+		File varscan_somatic_filter = "${sample}.VarScan.Somatic.filter.vcf"
+    File varscan_germline_filter = "${sample}.VarScan.Germline.filter.vcf"
+		File varscan_loh_filter = "${sample}.VarScan.LOH.filter.vcf"
+  }
+}

workflow.wdl

@@ -14,6 +14,10 @@ import "./tasks/MSIsensor.wdl" as MSIsensor
 import "./tasks/HRD.wdl" as HRD
 import "./tasks/TMB.wdl" as TMB
 
+import "./tasks/fastqc.wdl" as fastqc
+import "./tasks/fastqscreen.wdl" as fastqscreen
+import "./tasks/qualimap.wdl" as qualimap
+
 workflow {{ project_name }} {
   
   String sample_id
@@ -57,6 +61,16 @@ workflow {{ project_name }} {
   String cluster_2cpu_4gb
   String cluster_16cpu_32gb
   
+  Boolean qc
+  String fastqc_docker
+  String fastqscreen_docker
+  String qualimap_docker
+  File screen_ref_dir
+  File fastq_screen_conf
+
+  Boolean multi_caller
+  String varscan_docker
+
   if (tumor_fastq_1!= "") {
     call mapping.mapping as tumor_mapping {
       input:
@@ -128,6 +142,41 @@ workflow {{ project_name }} {
       disk_size=disk_size,
       cluster_config=cluster_16cpu_32gb
     }
+
+    if (qc){
+      call fastqc.fastqc as tumor_fastqc {
+        input:
+        sample=sample_id + '.T',
+        read1=tumor_fastq_1,
+        read2=tumor_fastq_2,
+        docker=fastqc_docker,
+        disk_size=disk_size,
+        cluster_config=cluster_2cpu_4gb
+      }
+      
+      call fastqscreen.fastq_screen as tumor_fastqscreen {
+        input:
+        sample=sample_id + '.T',
+        read1=tumor_fastq_1,
+        read2=tumor_fastq_2,
+        screen_ref_dir=screen_ref_dir,
+        fastq_screen_conf=fastq_screen_conf,
+        docker=fastqscreen_docker,
+        disk_size=disk_size,
+        cluster_config=cluster_2cpu_4gb
+      }
+      
+      call qualimap.qualimap as tumor_qualimap {
+        input:
+        sample=sample_id + '.T',
+        bam=tumor_Dedup.deduped_bam,
+        bai=tumor_Dedup.deduped_bam_index,
+        covered_bed=regions,
+        docker=qualimap_docker,
+        disk_size=disk_size,
+        cluster_config=cluster_16cpu_32gb
+      }
+    }
   }
   
   if (normal_fastq_1!= "") {
@@ -229,8 +278,43 @@ workflow {{ project_name }} {
       cluster_config=cluster_2cpu_4gb,
       disk_size=disk_size
     }
+
+    if (qc){
+      call fastqc.fastqc as normal_fastqc {
+        input:
+        sample=sample_id + '.N',
+        read1=normal_fastq_1,
+        read2=normal_fastq_2,
+        docker=fastqc_docker,
+        disk_size=disk_size,
+        cluster_config=cluster_2cpu_4gb
+      }
+      
+      call fastqscreen.fastq_screen as normal_fastqscreen {
+        input:
+        sample=sample_id + '.N',
+        read1=normal_fastq_1,
+        read2=normal_fastq_2,
+        screen_ref_dir=screen_ref_dir,
+        fastq_screen_conf=fastq_screen_conf,
+        docker=fastqscreen_docker,
+        disk_size=disk_size,
+        cluster_config=cluster_2cpu_4gb
+      }
+      
+      call qualimap.qualimap as normal_qualimap {
+        input:
+        sample=sample_id + '.N',
+        bam=normal_Dedup.deduped_bam,
+        bai=normal_Dedup.deduped_bam_index,
+        covered_bed=regions,
+        docker=qualimap_docker,
+        disk_size=disk_size,
+        cluster_config=cluster_16cpu_32gb
+      }
+    }
   }
-  
+
   call Manta.Manta as Manta {
     input:
     sample=sample_id,
@@ -353,4 +437,103 @@ workflow {{ project_name }} {
     cluster_config=cluster_2cpu_4gb,
     disk_size=disk_size
   }
+  
+  
+  call somatic.somatic as somatic {
+    input:
+    sample=sample_id,
+    normal_bam=normal_BQSR.recaled_bam,
+    normal_bam_index=normal_BQSR.recaled_bam_index,
+    tumor_bam=tumor_BQSR.recaled_bam,
+    tumor_bam_index=tumor_BQSR.recaled_bam_index,
+    ref_dir=ref_dir,
+    fasta=fasta,
+    docker=varscan_docker,
+    disk_size=disk_size,
+    cluster_config=cluster_16cpu_32gb
+  }
+  
+  call processSomatic.processSomatic as processSomatic {
+    input:
+    sample=sample_id,
+    varscan_snp=somatic.varscan_snp,
+    varscan_indel=somatic.varscan_indel,
+    docker=varscan_docker,
+    disk_size=disk_size,
+    cluster_config=cluster_16cpu_32gb
+  }
+  
+  call somaticFilter.somaticFilter as somaticFilter {
+    input:
+    sample=sample_id,
+    varscan_snp_somatic_hc=processSomatic.varscan_snp_somatic_hc,
+    varscan_snp_germline_hc=processSomatic.varscan_snp_germline_hc,
+    varscan_snp_loh_hc=processSomatic.varscan_snp_loh_hc,
+    varscan_indel_somatic_hc=processSomatic.varscan_indel_somatic_hc,
+    varscan_indel_germline_hc=processSomatic.varscan_indel_germline_hc,
+    varscan_indel_loh_hc=processSomatic.varscan_indel_loh_hc,
+    varscan_indel=somatic.varscan_indel,
+    docker=varscan_docker,
+    disk_size=disk_size,
+    cluster_config=cluster_16cpu_32gb
+  }
+  
+  call bcftools.bcftools as VarScan_bcftools {
+    input:
+    vcf=somaticFilter.varscan_somatic_filter,
+    fasta=fasta,
+    ref_dir=ref_dir,
+    docker=bcftools_docker,
+    cluster_config=cluster_2cpu_4gb,
+    disk_size=disk_size
+  }
+  
+  call ANNOVAR.ANNOVAR as VarScan_ANNOVAR {
+    input:
+    vcf=VarScan_bcftools.norm_vcf,
+    annovar_database=annovar_database,
+    docker=annovar_docker,
+    cluster_config=cluster_16cpu_32gb,
+    disk_size=disk_size
+  }
+  
+  call TNscope.TNscope as TNscope {
+    input:
+    SENTIEON_LICENSE=SENTIEON_LICENSE,
+    sample=sample_id,
+    normal_recaled_bam=normal_BQSR.recaled_bam,
+    normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
+    tumor_recaled_bam=tumor_BQSR.recaled_bam,
+    tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,
+    normal_name=sample_id + ".N",
+    tumor_name=sample_id + ".T",
+    fasta=fasta,
+    ref_dir=ref_dir,
+    regions=regions,
+    interval_padding=interval_padding,
+    dbsnp=dbsnp,
+    dbsnp_dir=dbsnp_dir,
+    docker=sentieon_docker,
+    cluster_config=cluster_16cpu_32gb,
+    disk_size=disk_size
+  }
+  
+  call bcftools.bcftools as TNscope_bcftools {
+    input:
+    vcf=TNscope.TNscope_vcf,
+    fasta=fasta,
+    ref_dir=ref_dir,
+    docker=bcftools_docker,
+    cluster_config=cluster_2cpu_4gb,
+    disk_size=disk_size
+  }
+  
+  call ANNOVAR.ANNOVAR as TNscope_ANNOVAR {
+    input:
+    vcf=TNscope_bcftools.norm_vcf,
+    annovar_database=annovar_database,
+    docker=annovar_docker,
+    cluster_config=cluster_16cpu_32gb,
+    disk_size=disk_size
+  }
 }