diff --git a/variants/cnvkit.sh b/variants/cnvkit.sh
index a728ad9cc23a8ad0d5015a0d2da36d82b2e6e7c5..c039906dcd21701313d13633bb7eeec54243e925 100755
--- a/variants/cnvkit.sh
+++ b/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" ]]
diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index b8699b0272243106981dc2093a514fd64a7b8b9e..5e02d9ebfdbeeb79081387dab5c82632ab641d44 100755
--- a/variants/germline_vc.sh
+++ b/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
diff --git a/variants/somatic_vc.sh b/variants/somatic_vc.sh
index 0689f7ebf3f6ae1399ecf5eabff3d1efd97c6c3a..b5813c72391bff8277fc7fed88b4d155fbd9bb6b 100755
--- a/variants/somatic_vc.sh
+++ b/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
diff --git a/variants/svcalling.sh b/variants/svcalling.sh
index 17830e7b4a84c303bffbf63a041495cd58588287..59119ba234bea4693c1247063361ec3837bd23ce 100755
--- a/variants/svcalling.sh
+++ b/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