option for manta failure, itdseek in svcalling with filtering

variants/cnvkit.sh

@@ -11,7 +11,7 @@ usage() {
   exit 1
 }
 OPTIND=1 # Reset OPTIND
-while getopts :b:p:n:t:r:uqh opt
+while getopts :b:p:n:d:t:r:uqh opt
 do
     case $opt in
         b) sbam=$OPTARG;;
@@ -33,6 +33,7 @@ fi
 # Check for mandatory options
 if [[ -z $pair_id ]] || [[ -z $sbam ]]
 then
+    "missing pair_id or bam"
     usage
 fi
 NPROC=$SLURM_CPUS_ON_NODE
@@ -42,6 +43,7 @@ then
 fi
 if [[ -z $paneldir ]]
 then
+    echo "missing panel dir"
     usage
 fi
 if [[ -s "${index_path}/genome.fa" ]]

variants/germline_vc.sh

@@ -125,7 +125,7 @@ then
   for i in *.bam; do
       bamlist+="-I ${i} "
   done
-  gatk --java-options "-Xmx20g" Mutect2 $ponopt -R ${reffa} ${bamlist} --output ${pair_id}.mutect.vcf -RF AllowAllReadsReadFilter --independent-mates
+  gatk --java-options "-Xmx20g" Mutect2 $ponopt -R ${reffa} ${bamlist} --output ${pair_id}.mutect.vcf -RF AllowAllReadsReadFilter --independent-mates  --tmp-dir `pwd`
   gatk --java-options "-Xmx20g" FilterMutectCalls -R ${reffa} -V ${pair_id}.mutect.vcf -O ${pair_id}.mutect.filt.vcf
   vcf-sort ${pair_id}.mutect.filt.vcf | vcf-annotate -n --fill-type | java -jar $SNPEFF_HOME/SnpSift.jar filter -p '(GEN[*].DP >= 10)' | bgzip > ${pair_id}.mutect.vcf.gz
 
@@ -145,7 +145,12 @@ then
     done
     configManta.py $gvcflist --referenceFasta ${reffa} $mode --runDir manta
     manta/runWorkflow.py -m local -j $NPROC
-    configureStrelkaGermlineWorkflow.py $gvcflist --referenceFasta ${reffa} $mode --indelCandidates manta/results/variants/candidateSmallIndels.vcf.gz --runDir strelka
+    if [[ -f manta/results/variants/candidateSmallIndels.vcf.gz ]]
+    then
+	configureStrelkaGermlineWorkflow.py $gvcflist --referenceFasta ${reffa} $mode --indelCandidates manta/results/variants/candidateSmallIndels.vcf.gz --runDir strelka
+    else
+	configureStrelkaGermlineWorkflow.py $gvcflist --referenceFasta ${reffa} $mode --runDir strelka
+    fi
     strelka/runWorkflow.py -m local -j $NPROC
     bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.strelka2.vcf.gz strelka/results/variants/variants.vcf.gz
 fi

variants/somatic_vc.sh

@@ -97,7 +97,12 @@ if [ $algo == 'strelka2' ]
     mkdir manta strelka
     configManta.py --normalBam ${normal} --tumorBam ${tumor} --referenceFasta ${reffa} --runDir manta
     manta/runWorkflow.py -m local -j 8
-    configureStrelkaSomaticWorkflow.py --normalBam ${normal} --tumorBam ${tumor} --referenceFasta ${reffa} --targeted --indelCandidates manta/results/variants/candidateSmallIndels.vcf.gz --runDir strelka
+    if [[ -f manta/results/variants/candidateSmallIndels.vcf.gz ]]
+    then
+	configureStrelkaSomaticWorkflow.py --normalBam ${normal} --tumorBam ${tumor} --referenceFasta ${reffa} --targeted --indelCandidates manta/results/variants/candidateSmallIndels.vcf.gz --runDir strelka
+    else
+	configureStrelkaSomaticWorkflow.py --normalBam ${normal} --tumorBam ${tumor} --referenceFasta ${reffa} --targeted --indelCandidates --runDir strelka
+    fi
     strelka/runWorkflow.py -m local -j 8
     vcf-concat strelka/results/variants/*.vcf.gz | vcf-annotate -n --fill-type -n |vcf-sort |java -jar $SNPEFF_HOME/SnpSift.jar filter "(GEN[*].DP >= 10)" | perl -pe "s/TUMOR/${tid}/g" | perl -pe "s/NORMAL/${nid}/g" |bgzip > ${pair_id}.strelka2.vcf.gz
 fi

variants/svcalling.sh

@@ -11,7 +11,7 @@ usage() {
   exit 1
 }
 OPTIND=1 # Reset OPTIND
-while getopts :r:p:b:i:x:y:n:l:a:h opt
+while getopts :r:p:b:i:x:y:n:l:f:a:h opt
 do
     case $opt in
         r) index_path=$OPTARG;;
@@ -22,6 +22,7 @@ do
 	a) method=$OPTARG;;
         x) tid=$OPTARG;;
         y) nid=$OPTARG;;
+	f) filter=1;;
 	l) bed=$OPTARG;;
         h) usage;;
     esac
@@ -96,8 +97,7 @@ then
     bcftools concat -a -O v delly_dup.bcf delly_inv.bcf delly_tra.bcf delly_del.bcf delly_ins.bcf| vcf-sort -t temp > delly.vcf
     bgzip delly.vcf
     java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} delly.vcf | bgzip > ${pair_id}.delly.vcf.gz
-fi
-if [[ $method == 'svaba' ]]
+elif [[ $method == 'svaba' ]]
 then
     if [[ -n ${normal} ]]
     then
@@ -105,20 +105,19 @@ then
     else
 	svaba run -p $NPROC -G ${reffa} -t ${sbam} -a ${pair_id}
     fi
+    #Create SV FILE
     vcf-concat ${pair_id}.svaba.unfiltered*sv.vcf | vcf-sort -t temp > svaba.sv.vcf
     cat svaba.sv.vcf | java -jar $SNPEFF_HOME/SnpSift.jar filter "( GEN[*].AD[0] >= 20 )" | bgzip > svaba.vcf.gz
     tabix svaba.sv.vcf.gz
     bash $baseDir/norm_annot.sh -r ${index_path} -p svaba.sv -v svaba.sv.vcf.gz -s
     java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} svaba.sv.norm.vcf | bgzip > ${pair_id}.svaba.sv.vcf.gz
+    #Create INDEL FILE
     vcf-concat ${pair_id}.svaba.unfiltered*indel.vcf | vcf-sort -t temp > svaba.indel.vcf
     cat svaba.indel.vcf | java -jar $SNPEFF_HOME/SnpSift.jar filter "( GEN[*].AD[0] >= 20 )" | bgzip > svaba.indel.vcf.gz
     tabix svaba.indel.vcf.gz
     bash $baseDir/norm_annot.sh -r ${index_path} -p svaba.indel -v svaba.indel.vcf.gz -s
     java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} svaba.indel.norm.vcf | bgzip > ${pair_id}.svaba.vcf.gz
-
-fi
-
-if [[ $method == 'lumpy' ]]
+elif [[ $method == 'lumpy' ]]
 then
     #MAKE FILES FOR LUMPY
     samtools sort -@ $NPROC -n -o namesort.bam ${sbam}
@@ -137,8 +136,7 @@ then
 	speedseq sv -t $NPROC -o lumpy -R ${reffa} -B ${sbam} -D discordants.bam -S splitters.bam -x ${index_path}/exclude_alt.bed   
     fi
     java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} lumpy.sv.vcf.gz | java -jar $SNPEFF_HOME/SnpSift.jar filter " ( GEN[*].DV >= 20 )" | bgzip > ${pair_id}.lumpy.vcf.gz
-fi
-if [[ $method == 'pindel' ]]
+elif [[ $method == 'pindel' ]]
 then
     module load pindel/0.2.5-intel
     genomefiledate=`find ${reffa} -maxdepth 0 -printf "%TY%Tm%Td\n"`
@@ -157,12 +155,18 @@ then
     java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} ${pair_id}.indel.vcf |bgzip > ${pair_id}.pindel_indel.vcf.gz
     java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} ${pair_id}.dup.vcf | bedtools intersect -header -b ${bed} -a stdin | bgzip > ${pair_id}.pindel_tandemdup.vcf.gz
     java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} ${pair_id}.sv.vcf | bgzip > ${pair_id}.pindel_sv.vcf.gz
-fi
-if [[ $method == 'itdseek' ]]
+elif [[ $method == 'itdseek' ]]
 then
     stexe=`which samtools`
     samtools view -@ $NPROC -L ${bed} ${sbam} | itdseek.pl --refseq ${reffa} --samtools ${stexe} --bam ${sbam} | vcf-sort | bedtools intersect -header -b ${bed} -a stdin | bgzip > ${pair_id}.itdseek.vcf.gz
-
+    
     tabix ${pair_id}.itdseek.vcf.gz
     bcftools norm --fasta-ref $reffa -m - -Ov ${pair_id}.itdseek.vcf.gz | java -Xmx30g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} - |bgzip > ${pair_id}.itdseek_tandemdup.vcf.gz
+    if [[ $filter == 1 ]]
+    then
+	perl $baseDir/filter_itdseeker.pl -t ${pair_id} -d ${pair_id}.itdseek_tandemdup.vcf.gz
+	mv ${pair_id}.itdseek_tandemdup.vcf.gz ${pair_id}.itdseek_tandemdup.unfilt.vcf.gz
+	mv ${pair_id}.itdseek_tandemdup.pass.vcf ${pair_id}.itdseek_tandemdup.vcf
+	bgzip ${pair_id}.itdseek_tandemdup.vcf
+    fi
 fi