From 2f76edc9a1253f9c68c67fe648dfd4438289b834 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 19 Mar 2020 16:22:48 -0500
Subject: [PATCH] update delly svaba sv calling filter
---
variants/filter_delly.pl | 4 ++++
variants/filter_svaba.pl | 2 +-
variants/svcalling.sh | 10 +++++-----
3 files changed, 10 insertions(+), 6 deletions(-)
diff --git a/variants/filter_delly.pl b/variants/filter_delly.pl
index 95ea52e..8cb2ec9 100755
--- a/variants/filter_delly.pl
+++ b/variants/filter_delly.pl
@@ -99,6 +99,9 @@ W1:while (my $line = <IN>) {
}
}
my $newannot = join(";",@nannot);
+ if ($filter ne 'PASS') {
+ $filter = 'FailedQC;'.$filter;
+ }
if ($hash{SVTYPE} eq 'INS' || ($hash{SVTYPE} eq 'DEL' && $keepforvcf !~ m/&/)) {
print VCFOUT join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$newannot,
$format,@gts),"\n";
@@ -106,6 +109,7 @@ W1:while (my $line = <IN>) {
my ($allele,$effect,$impact,$gene,$geneid,$feature,
$featureid,$biotype,$rank,$codon,$aa,$pos_dna,$len_cdna,
$cds_pos,$cds_len,$aapos,$aalen,$distance,$err) = split(/\|/,$keeptrx);
+
print DELFUS join("\t",$chrom,$pos,$hash{CHR2},$hash{END},$effect,$gene,$biotype,$filter,$format,@gts),"\n";
}
}
diff --git a/variants/filter_svaba.pl b/variants/filter_svaba.pl
index 116f7da..19565c2 100755
--- a/variants/filter_svaba.pl
+++ b/variants/filter_svaba.pl
@@ -110,7 +110,7 @@ W1:while (my $line = <IN>) {
my $newannot = join(";",@nannot);
if ($hash{SVTYPE} eq 'INS' || ($hash{SVTYPE} eq 'DEL' && $keepforvcf !~ m/&/)) {
if ($filter =~ m/LOWMAPQ|LowQual/i) {
- $filter = 'FailedQC'.$filter;
+ $filter = 'FailedQC;'.$filter;
}
print VCFOUT join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$newannot,
$format,@gts),"\n";
diff --git a/variants/svcalling.sh b/variants/svcalling.sh
index 41671c5..d2de989 100755
--- a/variants/svcalling.sh
+++ b/variants/svcalling.sh
@@ -96,12 +96,12 @@ then
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}.dgf.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
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}.delly.potentialfusion.txt ${pair_id}.dgf.txt |sort -u > ${pair_id}.delly.genefusion.txt
+ bgzip -f ${pair_id}.delly.vcf
+ zgrep '#CHROM' ${pair_id}.delly.vcf.gz > ${pair_id}.delly.genefusion.txt
+ cat ${pair_id}.delly.potentialfusion.txt ${pair_id}.dgf.txt |sort -u >> ${pair_id}.delly.genefusion.txt
fi
elif [[ $method == 'svaba' ]]
then
@@ -122,11 +122,11 @@ 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}.sgf.txt
mv ${pair_id}.svaba.vcf.gz ${pair_id}.svaba.ori.vcf.gz
perl $baseDir/filter_svaba.pl -t $tid -p $pair_id -i ${pair_id}.svaba.ori.vcf.gz -s ${pair_id}.svaba.sv.vcf.gz
bgzip ${pair_id}.svaba.vcf
+ zgrep '#CHROM' ${pair_id}.svaba.sv.vcf.gz > ${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' ]]
--
GitLab