diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index 5e02d9ebfdbeeb79081387dab5c82632ab641d44..f8b2eaa1f7412c751c0a289ca4bdca5a71a2ba98 100755
--- a/variants/germline_vc.sh
+++ b/variants/germline_vc.sh
@@ -82,7 +82,7 @@ then
vcf-annotate -n --fill-type ${pair_id}.vcf.gz | bcftools norm -c s -f ${reffa} -w 10 -O v -o sam.vcf
java -jar $PICARD/picard.jar SortVcf I=sam.vcf O=${pair_id}.sam.vcf R=${reffa} CREATE_INDEX=TRUE
bgzip ${pair_id}.sam.vcf
-elif [[ $algo == 'freebayes' ]]
+elif [[ $algo == 'fb' ]]
then
module load freebayes/gcc/1.2.0 parallel/20150122
bamlist=''
@@ -90,7 +90,7 @@ then
bamlist="$bamlist --bam ${PWD}/${i}"
done
cut -f 1 ${index_path}/genomefile.5M.txt | parallel --delay 2 -j $NPROC "freebayes -f ${index_path}/genome.fa --min-mapping-quality 0 --min-base-quality 20 --min-coverage 10 --min-alternate-fraction 0.01 -C 3 --use-best-n-alleles 3 -r {} ${bamlist} > fb.{}.vcf"
- vcf-concat fb.*.vcf | vcf-sort | vcf-annotate -n --fill-type | bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.freebayes.vcf.gz -
+ vcf-concat fb.*.vcf | vcf-sort | vcf-annotate -n --fill-type | bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.fb.vcf.gz -
elif [[ $algo == 'platypus' ]]
then
module load platypus/gcc/0.8.1
@@ -117,7 +117,7 @@ then
gatk --java-options "-Xmx32g" GenotypeGVCFs -V gendb://gendb -R ${reffa} -D ${gatk4_dbsnp} -O gatk.vcf
bcftools norm -c s -f ${reffa} -w 10 -O v gatk.vcf | vcf-annotate -n --fill-type gatk.vcf | bgzip > ${pair_id}.gatk.vcf.gz
tabix ${pair_id}.gatk.vcf.gz
-elif [ $algo == 'mutect2' ]
+elif [ $algo == 'mutect' ]
then
gatk4_dbsnp=${index_path}/clinseq_prj/dbSnp.gatk4.vcf.gz
module load gatk/4.1.4.0
diff --git a/variants/somatic_vc.sh b/variants/somatic_vc.sh
index b5813c72391bff8277fc7fed88b4d155fbd9bb6b..f441cdf44fbf8d912b8ecef9df99e3f373eaa2b5 100755
--- a/variants/somatic_vc.sh
+++ b/variants/somatic_vc.sh
@@ -115,7 +115,7 @@ if [ $algo == 'virmid' ]
module rm java/oracle/jdk1.7.0_51
module load snpeff/4.3q
vcf-concat *gt.vcf | vcf-sort | vcf-annotate -n --fill-type -n | java -jar $SNPEFF_HOME/SnpSift.jar filter '((NDP >= 10) & (DDP >= 10))' | perl -pe "s/TUMOR/${tid}/g" | perl -pe "s/NORMAL/${nid}/g" | bgzip > ${pair_id}.virmid.vcf.gz
-elif [ $algo == 'mutect2' ]
+elif [ $algo == 'mutect' ]
then
gatk4_dbsnp=${index_path}/clinseq_prj/dbSnp.gatk4.vcf.gz
module load gatk/4.1.4.0 picard/2.10.3 snpeff/4.3q samtools/gcc/1.8 vcftools/0.1.14
diff --git a/variants/svcalling.sh b/variants/svcalling.sh
index 59119ba234bea4693c1247063361ec3837bd23ce..5da21c2084f521cbb7d5680fcf739d4e40b1e922 100755
--- a/variants/svcalling.sh
+++ b/variants/svcalling.sh
@@ -64,39 +64,44 @@ mkdir temp
if [[ $method == 'delly' ]]
then
- module load delly2/v0.7.7-multi
+ #module load delly2/v0.7.7-multi
if [[ -n ${normal} ]]
then
#RUN DELLY
echo -e "${nid}\tcontrol"> samples.tsv
echo -e "${tid}\ttumor" >> samples.tsv
- delly2 call -t BND -o delly_translocations.bcf -q 30 -g ${reffa} ${sbam} ${normal}
- delly2 call -t DUP -o delly_duplications.bcf -q 30 -g ${reffa} ${sbam} ${normal}
- delly2 call -t INV -o delly_inversions.bcf -q 30 -g ${reffa} ${sbam} ${normal}
- delly2 call -t DEL -o delly_deletion.bcf -q 30 -g ${reffa} ${sbam} ${normal}
- delly2 call -t INS -o delly_insertion.bcf -q 30 -g ${reffa} ${sbam} ${normal}
- delly2 filter -t BND -o delly_tra.bcf -f somatic -s samples.tsv delly_translocations.bcf
- delly2 filter -t DUP -o delly_dup.bcf -f somatic -s samples.tsv delly_duplications.bcf
- delly2 filter -t INV -o delly_inv.bcf -f somatic -s samples.tsv delly_inversions.bcf
- delly2 filter -t DEL -o delly_del.bcf -f somatic -s samples.tsv delly_deletion.bcf
- delly2 filter -t INS -o delly_ins.bcf -f somatic -s samples.tsv delly_insertion.bcf
+ delly2 call -t BND -o ${pair_id}.delly_translocations.bcf -q 30 -g ${reffa} ${sbam} ${normal}
+ delly2 call -t DUP -o ${pair_id}.delly_duplications.bcf -q 30 -g ${reffa} ${sbam} ${normal}
+ delly2 call -t INV -o ${pair_id}.delly_inversions.bcf -q 30 -g ${reffa} ${sbam} ${normal}
+ delly2 call -t DEL -o ${pair_id}.delly_deletion.bcf -q 30 -g ${reffa} ${sbam} ${normal}
+ delly2 call -t INS -o ${pair_id}.delly_insertion.bcf -q 30 -g ${reffa} ${sbam} ${normal}
+ #delly2 filter -o ${pair_id}.delly_tra.bcf -f somatic -s samples.tsv ${pair_id}.delly_translocations.bcf
+ #delly2 filter -o ${pair_id}.delly_dup.bcf -f somatic -s samples.tsv ${pair_id}.delly_duplications.bcf
+ #delly2 filter -o ${pair_id}.delly_inv.bcf -f somatic -s samples.tsv ${pair_id}.delly_inversions.bcf
+ #delly2 filter -o ${pair_id}.delly_del.bcf -f somatic -s samples.tsv ${pair_id}.delly_deletion.bcf
+ #delly2 filter -o ${pair_id}.delly_ins.bcf -f somatic -s samples.tsv ${pair_id}.delly_insertion.bcf
else
#RUN DELLY
- delly2 call -t BND -o delly_translocations.bcf -q 30 -g ${reffa} ${sbam}
- delly2 call -t DUP -o delly_duplications.bcf -q 30 -g ${reffa} ${sbam}
- delly2 call -t INV -o delly_inversions.bcf -q 30 -g ${reffa} ${sbam}
- delly2 call -t DEL -o delly_deletion.bcf -q 30 -g ${reffa} ${sbam}
- delly2 call -t INS -o delly_insertion.bcf -q 30 -g ${reffa} ${sbam}
- delly2 filter -t BND -o delly_tra.bcf -f germline delly_translocations.bcf
- delly2 filter -t DUP -o delly_dup.bcf -f germline delly_duplications.bcf
- delly2 filter -t INV -o delly_inv.bcf -f germline delly_inversions.bcf
- delly2 filter -t DEL -o delly_del.bcf -f germline delly_deletion.bcf
- delly2 filter -t INS -o delly_ins.bcf -f germline delly_insertion.bcf
+ delly2 call -t BND -o ${pair_id}.delly_translocations.bcf -q 30 -g ${reffa} ${sbam}
+ delly2 call -t DUP -o ${pair_id}.delly_duplications.bcf -q 30 -g ${reffa} ${sbam}
+ delly2 call -t INV -o ${pair_id}.delly_inversions.bcf -q 30 -g ${reffa} ${sbam}
+ delly2 call -t DEL -o ${pair_id}.delly_deletion.bcf -q 30 -g ${reffa} ${sbam}
+ delly2 call -t INS -o ${pair_id}.delly_insertion.bcf -q 30 -g ${reffa} ${sbam}
+ #delly2 filter -o ${pair_id}.delly_tra.bcf -f germline ${pair_id}.delly_translocations.bcf
+ #delly2 filter -o ${pair_id}.delly_dup.bcf -f germline ${pair_id}.delly_duplications.bcf
+ #delly2 filter -o ${pair_id}.delly_inv.bcf -f germline ${pair_id}.delly_inversions.bcf
+ #delly2 filter -o ${pair_id}.delly_del.bcf -f germline ${pair_id}.delly_deletion.bcf
+ #delly2 filter -o ${pair_id}.delly_ins.bcf -f germline ${pair_id}.delly_insertion.bcf
fi
#MERGE DELLY AND MAKE BED
- 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
+
+ bcftools concat -a -O v ${pair_id}.delly_duplications.bcf ${pair_id}.delly_inversions.bcf ${pair_id}.delly_translocations.bcf | vcf-sort -t temp | bgzip > ${pair_id}.delly.svar.vcf.gz
+ bash $baseDir/norm_annot.sh -r ${index_path} -p ${pair_id}.delly.sv -v ${pair_id}.delly.svar.vcf.gz -s
+ java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} ${pair_id}.delly.sv.norm.vcf.gz | bgzip > ${pair_id}.delly.sv.vcf.gz
+ bcftools concat -a -O v ${pair_id}.delly_deletion.bcf ${pair_id}.delly_insertion.bcf | vcf-sort -t temp | bgzip > ${pair_id}.dellyindel.vcf.gz
+ bash $baseDir/norm_annot.sh -r ${index_path} -p ${pair_id}.delly.indel -v ${pair_id}.dellyindel.vcf.gz -s
+ java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} ${pair_id}.delly.indel.norm.vcf.gz | bgzip > ${pair_id}.delly.vcf.gz
+
elif [[ $method == 'svaba' ]]
then
if [[ -n ${normal} ]]
@@ -107,16 +112,16 @@ then
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
+ bgzip -f svaba.sv.vcf
+ tabix -f 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
+ java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} svaba.sv.norm.vcf.gz | java -jar $SNPEFF_HOME/SnpSift.jar filter "( GEN[*].AD[1] >= 20 )" | 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
+ bgzip -f svaba.indel.vcf
+ tabix -f 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
+ java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} svaba.indel.norm.vcf.gz | java -jar $SNPEFF_HOME/SnpSift.jar filter "( GEN[*].AD[1] >= 20 )" | bgzip > ${pair_id}.svaba.vcf.gz
elif [[ $method == 'lumpy' ]]
then
#MAKE FILES FOR LUMPY
diff --git a/variants/uniform_vcf_gt.pl b/variants/uniform_vcf_gt.pl
index 9bb7953fdf9d677026a047a4390a3aa9db8bddbe..7b7a6f4814461fd8bf5a0ea380220cc802cbf612 100755
--- a/variants/uniform_vcf_gt.pl
+++ b/variants/uniform_vcf_gt.pl
@@ -49,14 +49,25 @@ while (my $line = <VCF>) {
foreach (@alts) {
$gtdata{DP} += $_;
}
- } elsif ($gtdata{AD} =~ m/^\d+$/ && $gtdata{DP}){
+ } elsif (exists $gtdata{DV} && exists $gtdata{RV}) {
+ $gtdata{AO} = $gtdata{DV} + $gtdata{RV};
+ $gtdata{RO} = $gtdata{DR} + $gtdata{RR};
+ $gtdata{AD} = join(',',$gtdata{RO},$gtdata{AO});
+ $gtdata{DP} = $gtdata{RO}+$gtdata{AO};
+
+ } elsif (exists $gtdata{DR} && exists $gtdata{SR}){
$gtdata{AO} = $gtdata{AD};
- $gtdata{RO} = $gtdata{DP} - $gtdata{AD};
+ $gtdata{DP} = $gtdata{AO} unless $gtdata{DP};
+ if ($gtdata{DP} > $gtdata{AD}) {
+ $gtdata{RO} = $gtdata{DP} - $gtdata{AD};
+ } else {
+ $gtdata{RO} = 0;
+ }
$gtdata{AD} = join(',',$gtdata{RO},$gtdata{AO});
} elsif (exists $gtdata{NR} && exists $gtdata{NV}) {
- $gtdata{DP} = $gtdata{NR};
- $gtdata{AO} = $gtdata{NV};
- $gtdata{RO} = $gtdata{DP} - $gtdata{AO};
+ $gtdata{DP} = $gtdata{NR};
+ $gtdata{AO} = $gtdata{NV};
+ $gtdata{RO} = $gtdata{DP} - $gtdata{AO};
} elsif (exists $gtdata{AO} && exists $gtdata{RO}) {
$gtdata{AD} = join(',',$gtdata{RO},$gtdata{AO});
$gtdata{DP} = $gtdata{RO};