From 488f3a25c5501ad2592f7b44efe84d4373e0fc17 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 19 Mar 2020 11:27:13 -0500
Subject: [PATCH] sv filtering
---
variants/filter_delly.pl | 3 ++-
variants/filter_svaba.pl | 3 ++-
variants/svcalling.sh | 21 ++++++++++++---------
3 files changed, 16 insertions(+), 11 deletions(-)
diff --git a/variants/filter_delly.pl b/variants/filter_delly.pl
index 4d6cffc..95ea52e 100755
--- a/variants/filter_delly.pl
+++ b/variants/filter_delly.pl
@@ -15,7 +15,7 @@ W1:while (my $line = <IN>) {
chomp($line);
if ($line =~ m/^#/) {
if ($line =~ m/^#CHROM/) {
- print OUT "##INFO=<ID=AF,Number=A,Type=Integer,Description=\"Alternate allele observation frequency\">\n";
+ print VCFOUT "##INFO=<ID=AF,Number=A,Type=Integer,Description=\"Alternate allele observation frequency\">\n";
my @header = split(/\t/,$line);
($chrom, $pos,$id,$ref,$alt,$score,
$filter,$info,$format,@gtheader) = split(/\t/, $line);
@@ -29,6 +29,7 @@ W1:while (my $line = <IN>) {
}
}
print VCFOUT $line,"\n";
+ next;
}
my ($chrom, $pos,$id,$ref,$alt,$score,
$filter,$annot,$format,@gts) = split(/\t/, $line);
diff --git a/variants/filter_svaba.pl b/variants/filter_svaba.pl
index f34ce1c..474046b 100755
--- a/variants/filter_svaba.pl
+++ b/variants/filter_svaba.pl
@@ -15,7 +15,7 @@ W1:while (my $line = <IN>) {
chomp($line);
if ($line =~ m/^#/) {
if ($line =~ m/^#CHROM/) {
- print OUT "##INFO=<ID=AF,Number=A,Type=Integer,Description=\"Alternate allele observation frequency\">\n";
+ print VCFOUT "##INFO=<ID=AF,Number=A,Type=Integer,Description=\"Alternate allele observation frequency\">\n";
my @header = split(/\t/,$line);
($chrom, $pos,$id,$ref,$alt,$score,
$filter,$info,$format,@gtheader) = split(/\t/, $line);
@@ -29,6 +29,7 @@ W1:while (my $line = <IN>) {
}
}
print VCFOUT $line,"\n";
+ next;
}
my ($chrom, $pos,$id,$ref,$alt,$score,
$filter,$annot,$format,@gts) = split(/\t/, $line);
diff --git a/variants/svcalling.sh b/variants/svcalling.sh
index 7ec4c1c..043a86c 100755
--- a/variants/svcalling.sh
+++ b/variants/svcalling.sh
@@ -77,7 +77,6 @@ then
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
else
- $tid=
#RUN DELLY
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}
@@ -87,19 +86,23 @@ then
#delly2 filter -o ${pair_id}.delly_tra.bcf -f germline ${pair_id}.delly_translocations.bcf
fi
#MERGE DELLY AND MAKE BED
-
+
bcftools concat -a -O v ${pair_id}.delly_duplications.bcf ${pair_id}.delly_inversions.bcf ${pair_id}.delly_translocations.bcf ${pair_id}.delly_deletion.bcf ${pair_id}.delly_insertion.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 -jar $SNPEFF_HOME/SnpSift.jar filter "( GEN[*].DP >= 20 )" ${pair_id}.delly.sv.norm.vcf.gz | java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} - | bgzip > ${pair_id}.delly.vcf.gz
if [[ $filter == 1 ]]
then
+ if [[ -z $tid ]]
+ then
+ tid=`samtools view -H ${sbam} |grep '^@RG' |perl -pi -e 's/\t/\n/g' |grep ID |cut -f 2 -d ':'`
+ fi
zgrep '#CHROM' ${pair_id}.delly.vcf.gz > ${pair_id}.delly.genefusion.txt
- zcat ${pair_id}.delly.vcf.gz | $SNPEFF_HOME/scripts/vcfEffOnePerLine.pl |java -jar $SNPEFF_HOME/SnpSift.jar extractFields - CHROM POS CHR2 END ANN[*].EFFECT ANN[*].GENE ANN[*].BIOTYPE FILTER FORMAT GEN[*] |grep -E 'gene_fusion|feature_fusion' | sort -u >> ${pair_id}.delly.genefusion.txt
+ zcat ${pair_id}.delly.vcf.gz | $SNPEFF_HOME/scripts/vcfEffOnePerLine.pl |java -jar $SNPEFF_HOME/SnpSift.jar extractFields - CHROM POS CHR2 END ANN[*].EFFECT ANN[*].GENE ANN[*].BIOTYPE FILTER FORMAT GEN[*] |grep -E 'gene_fusion|feature_fusion' | sort -u >> ${pair_id}.dgf.txt
mv ${pair_id}.delly.vcf.gz ${pair_id}.delly.ori.vcf.gz
- bash $baseDir/filter_delly.pl -t $tid -p $pair_id -i ${pair_id}.delly.ori.vcf.gz
+ perl $baseDir/filter_delly.pl -t $tid -p $pair_id -i ${pair_id}.delly.ori.vcf.gz
bgzip ${pair_id}.delly.vcf
- cat ${pair_id}.potentialfusion.txt >> ${pair_id}.delly.genefusion.txt
- fi
+ cat ${pair_id}.delly.potentialfusion.txt ${pair_id}.dgf.txt |sort -u > ${pair_id}.delly.genefusion.txt
+ fi
elif [[ $method == 'svaba' ]]
then
if [[ -n ${normal} ]]
@@ -120,11 +123,11 @@ then
if [[ $filter == 1 ]]
then
zgrep '#CHROM' ${pair_id}.svaba.sv.vcf.gz > ${pair_id}.svaba.genefusion.txt
- zcat ${pair_id}.svaba.sv.vcf.gz | $SNPEFF_HOME/scripts/vcfEffOnePerLine.pl |java -jar $SNPEFF_HOME/SnpSift.jar extractFields - CHROM POS ALT ID ANN[*].EFFECT ANN[*].GENE ANN[*].BIOTYPE FILTER FORMAT GEN[*] |grep -E 'gene_fusion|feature_fusion' | sort -u >> ${pair_id}.svaba.genefusion.txt
+ zcat ${pair_id}.svaba.sv.vcf.gz | $SNPEFF_HOME/scripts/vcfEffOnePerLine.pl |java -jar $SNPEFF_HOME/SnpSift.jar extractFields - CHROM POS ALT ID ANN[*].EFFECT ANN[*].GENE ANN[*].BIOTYPE FILTER FORMAT GEN[*] |grep -E 'gene_fusion|feature_fusion' | sort -u >> ${pair_id}.sgf.txt
mv ${pair_id}.svaba.vcf.gz ${pair_id}.svaba.ori.vcf.gz
- bash $baseDir/filter_svaba.pl -t $tid -p $pair_id -i ${pair_id}.svaba.ori.vcf.gz
+ perl $baseDir/filter_svaba.pl -t $tid -p $pair_id -i ${pair_id}.svaba.ori.vcf.gz -v
bgzip ${pair_id}.svaba.vcf
- cat ${pair_id}.potentialfusion.txt >> ${pair_id}.svaba.genefusion.txt
+ cat ${pair_id}.svaba.potentialfusion.txt ${pair_id}.sgf.txt | sort -u >> ${pair_id}.svaba.genefusion.txt
fi
elif [[ $method == 'lumpy' ]]
then
--
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