融合，cnv 完善

2023-08-29 10:31:06 +08:00 · 2023-08-29 10:31:06 +08:00 · d0335deb18
parent 6335842576
commit d0335deb18
5 changed files with 89 additions and 37 deletions
--- a/pipeline.wdl
+++ b/pipeline.wdl
@ -1,6 +1,8 @@
 import "./wdl/task.wdl" as mytask
 import "./wdl/qc.wdl"
 import "./wdl/alignment.wdl"
+import "./wdl/statistics.wdl"
+

 workflow pipeline {

@ -45,6 +47,20 @@ workflow pipeline {
            outputDir=workdir
    }

+    call statistics.statistics as statistics {
+        input:
+            tumor=tumor,
+            tumor_rmdupBam=alignment.tumor_rmdupBam,
+
+            normal=normal,
+            normal_rmdupBam=alignment.normal_rmdupBam,
+
+            ref=ref,
+            bed=bed,
+            outputDir=workdir,
+            codesDir=codesDir
+    }
+
    call mytask.mutation_calling as mutation_calling {
        input:
            name=tumor,
@ -80,17 +96,8 @@ workflow pipeline {
            outputDir=workdir,
            rmdupBam=alignment.tumor_rmdupBam,
            cancer=cancer,
-            project=project
-    }
-
-    call mytask.tumor_content as tumor_content {
-        input:
-            name=tumor,
-            tumor_pileup=alignment.tumor_pileup,
-            normal_pileup=alignment.normal_pileup,
-            ref=ref,
-            outputDir=workdir,
-            codesDir=codesDir,
+            project=project,
+            tumor_bamdst_depth=statistics.tumor_bamdst_depth
    }

    call mytask.cnvkit as cnvkit {
@ -106,7 +113,6 @@ workflow pipeline {
            cancer=cancer,
            codesDir=codesDir,
            project=project,
-            purity=tumor_content.purity
    }

    call mytask.chemo as chemo {
--- a/script/info.txt
+++ b/script/info.txt
@ -0,0 +1,3 @@
+project	probe	mutation	splicing	promoter	cnv	fusion	long_indel	chemotherapy_drug
+160gene	/dataseq/jmdna/database/bed/160.bed	AKT1/ALK/APC/ATM/BARD1/BRAF/BRCA1/BRCA2/BRIP1/CCND1/CCND2/CCND3/CDK12/CDK4/CDK6/CDKN2A/CHEK1/CHEK2/CSF1R/CTNNB1/DDR2/EGFR/ERBB2/ERBB3/ERBB4/FANCL/FBXW7/FGFR1/FGFR2/FGFR3/FLT3/GNA11/GNAQ/HRAS/IDH1/IDH2/JAK1/JAK2/JAK3/KDR/KIT/KRAS/MAP2K1/MET/MTOR/NF1/NRAS/NTRK1/NTRK2/NTRK3/PALB2/PDGFRA/PDGFRB/PIK3CA/PTEN/RAD51B/RAD51C/RAD51D/RAD54L/RB1/RET/ROS1/SMAD4/SMO/STK11/TP53/TSC1/TSC2/VHL	MET	TERT	CDK4/EGFR/ERBB2/FGFR1/FGFR2/FGFR3/FLT3/MET/MDM2/MDM4/CDKN2A	ALK/NTRK1/NTRK2/NTRK3/RET/ROS1	BCL2L11	NA
+650gene	/dataseq/jmdna/database/bed/650.bed	ABL1/AKT1/AKT2/AKT3/ALK/APC/ARAF/ATM/BARD1/BRAF/BRCA1/BRCA2/BRIP1/BTK/CCND1/CCND2/CCND3/CDK12/CDK4/CDK6/CDKN2A/CDKN2B/CHEK1/CHEK2/CSF1R/CTNNB1/DDR2/EGFR/ERBB2/ERBB3/ERBB4/ESR1/EZH2/FANCL/FBXW7/FGFR1/FGFR2/FGFR3/FGFR4/FLT3/GNA11/GNAQ/HRAS/IDH1/IDH2/JAK1/JAK2/JAK3/KDR/KIT/KRAS/MAP2K1/MAP2K2/MET/MPL/MTOR/MYCN/MYD88/NF1/NF2/NRAS/NTRK1/NTRK2/NTRK3/PALB2/PDGFRA/PDGFRB/PIK3CA/PTCH1/PTEN/RAD51B/RAD51C/RAD51D/RAD54L/RAF1/RB1/RET/ROS1/SMAD4/SMARCB1/SMO/STK11/TP53/TSC1/TSC2/VHL	MET	TERT	CDK4/EGFR/ERBB2/FGFR1/FGFR2/FGFR3/FLT3/MET/MYCN/MDM2/MDM4/CDKN2A/CDKN2B	ALK/BRAF/FGFR1/FGFR2/FGFR3/NTRK1/NTRK2/NTRK3/RET/ROS1	BCL2L11 NA
--- a/wdl/qc.wdl
+++ b/wdl/qc.wdl
@ -10,8 +10,8 @@ task runqc {
        mkdir ${outputDir}/qc
        fi

-        fastp -i ${inputDir}/*_$name_*1.fq.gz -o ${outputDir}/qc/${name}_clean_R1.fq.gz \
-        -I ${inputDir}/*_$name_*2.fq.gz -O ${outputDir}/qc/${name}_clean_R2.fq.gz \
+        fastp -i ${inputDir}/*_${name}_*1.fq.gz -o ${outputDir}/qc/${name}_clean_R1.fq.gz \
+        -I ${inputDir}/*_${name}_*2.fq.gz -O ${outputDir}/qc/${name}_clean_R2.fq.gz \
        -w 10 \
        --correction \
        --overlap_len_require 10 \
--- a/wdl/statistics.wdl
+++ b/wdl/statistics.wdl
@ -0,0 +1,57 @@
+task runstatistics {
+    String name
+    String outputDir
+    String rmdupBam
+
+    String ref
+    String codesDir
+    String bed
+
+    command <<<
+
+        if [ ! -d ${outputDir}/qc/${name}_bamdst ];then
+        mkdir -p ${outputDir}/qc/${name}_bamdst
+        fi
+
+        samtools flagstat -@ 10 ${rmdupBam} >${outputDir}/qc/${name}.rmdup.flagstat
+        samtools stats --reference ${ref} -t ${bed} -@ 10 ${rmdupBam} > ${outputDir}/qc/${name}.rmdup.stat
+        bamdst -p ${bed} -o ${outputDir}/qc/${name}_bamdst ${rmdupBam}
+
+        Rscript ${codesDir}/InsertAndDepthStat.R \
+        ${outputDir}/qc/${name}_InsertAndDepthStat \
+        ${outputDir}/qc/${name}_bamdst/insertsize.plot \
+        ${outputDir}/qc/${name}_bamdst/depth_distribution.plot
+    >>>
+}
+
+workflow statistics {
+
+    String tumor
+    String tumor_rmdupBam
+
+    String? normal
+    String? normal_rmdupBam
+
+    String ref
+    String bed
+    String outputDir
+    String codesDir
+
+    scatter(name in [tumor, normal]) {
+        if (defined(name)) {
+            call runstatistics {
+                input:
+                    name=name,
+                    outputDir=outputDir,
+                    rmdupBam=if name==tumor then tumor_rmdupBam else normal_rmdupBam,
+                    ref=ref,
+                    codesDir=codesDir,
+                    bed=bed
+            }
+        }
+    }
+
+    output {
+        String tumor_bamdst_depth = "${outputDir}/qc/${tumor}_bamdst/depth.tsv.gz"
+    }
+}
--- a/wdl/task.wdl
+++ b/wdl/task.wdl
@ -125,8 +125,6 @@ task annovar {
        -o ${outputDir}/mutation/${name}.TandemRepeatAnnotator.vcf \
        --annotation TandemRepeatAnnotator

-        # -nt 10
-
        grep -v "^##" ${outputDir}/mutation/${name}.TandemRepeatAnnotator.vcf \
        |cut -f8| paste ${outputDir}/mutation/${name}.snp.indel.Somatic.anno.hg19_multianno.txt  - \
        > ${outputDir}/mutation/${name}.snp.indel.Somatic.annoall.hg19_multianno.txt
@ -161,6 +159,7 @@ task fusion {
    String rmdupBam
    String cancer
    String project
+    String tumor_bamdst_depth

    command <<<

@ -178,7 +177,7 @@ task fusion {
        > ${outputDir}/fusion/${name}.splitters.bam

        lumpyexpress \
-        -B ${rmdupBam}\
+        -B ${rmdupBam} \
        -S ${outputDir}/fusion/${name}.splitters.bam \
        -D ${outputDir}/fusion/${name}.discordants.bam \
        -o ${outputDir}/fusion/${name}.fusion.vcf
@ -199,7 +198,7 @@ task fusion {
        -operation g \
        --outfile ${outputDir}/fusion/${name}.fusion

-        perl ${codesDir}/fusion.reanno.pl ${outputDir}/qc/${name}_bamdst/depth.tsv.gz ${outputDir} ${name}
+        perl ${codesDir}/fusion.reanno.pl ${tumor_bamdst_depth} ${outputDir} ${name}
        perl /home/jm001/test_duantao/database_update/codes/682/fusion_targetTherapy.pl ${codesDir} ${name} ${outputDir} ${project} ${cancer}

    >>>
@ -251,7 +250,6 @@ task cnvkit {
    String cancer
    String codesDir
    String project
-    String purity
    String accessBed = "/dataseq/jmdna/software/cnvkit-0.9.7/data/access-5k-mappable.hg19.bed"
    String annotateGene = "/dataseq/jmdna/software/cnvkit-0.9.7/data/refFlat.txt"

@ -277,18 +275,6 @@ task cnvkit {
        --title ${tumor}.cns \
        -o ${outputDir}/cnvkit/${tumor}.cnv.png

-        if [ -e "${outputDir}/qc/sequenza/${tumor}_confints_CP.txt" ]; then
-        # absolute copy number
-        cnvkit.py call \
-        -m clonal \
-        ${outputDir}/cnvkit/${tumor}.rmdup.cns \
-        -y \
-        --purity `head -n2 ${outputDir}/qc/sequenza/${tumor}_confints_CP.txt |tail -n1|cut -f1` \
-        --drop-low-coverage  \
-        --filter ampdel \
-        -o ${outputDir}/cnvkit/${tumor}.rmdup.cns.cn.hc
-        fi
-
        perl ${codesDir}/log2_cn.pl ${outputDir}/cnvkit/${tumor}.rmdup.cns ${outputDir}/cnvkit/${tumor}.rmdup.cns.cn
        perl /home/jm001/test_duantao/database_update/codes/682/cnv_targetTherapy.pl ${codesDir} ${tumor} ${outputDir} ${project} ${cancer}
    >>>
@ -323,14 +309,14 @@ task msi {
    String normal_rmdupBam

    command <<<
-        if [ ! -d ${outputDir}/MSI ];then
-        mkdir ${outputDir}/MSI
+        if [ ! -d ${outputDir}/msi ];then
+        mkdir ${outputDir}/msi
        fi

        msisensor2 msi -d /dataseq/jmdna/software/msisensor2/hg19.microsatellites.list \
-        -n ${outputDir}/alignment/${normal_rmdupBam} \
-        -t ${outputDir}/alignment/${tumor_rmdupBam} \
-        -e ${bed} -b 10 -o ${outputDir}/MSI/${name}.msi
+        -n ${normal_rmdupBam} \
+        -t ${tumor_rmdupBam} \
+        -e ${bed} -b 10 -o ${outputDir}/msi/${name}.msi

    >>>
    output {
@ -385,4 +371,4 @@ task neoantigen {
    output {
        String neoantigen = "${outputDir}/neoantigen/MHC_Class_I/${name}.all_epitopes.netchop.txt"
    }
-}
+}