From dd30007d4cb2237624cc72a35ca28d6ea8f14baf Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 25 Sep 2020 18:41:20 -0500
Subject: [PATCH] update svcalling
---
variants/filter_svaba.pl | 28 ++++++++++++----------------
variants/svcalling.sh | 4 ++--
2 files changed, 14 insertions(+), 18 deletions(-)
diff --git a/variants/filter_svaba.pl b/variants/filter_svaba.pl
index e962570..72a2eb3 100755
--- a/variants/filter_svaba.pl
+++ b/variants/filter_svaba.pl
@@ -41,11 +41,11 @@ W1:while (my $line = <IN>) {
$hash{$key} = $val unless ($hash{$key});
}
if (length($alt) > length($ref)) {
- $hash{SVTYPE} = "INS";
- $hash{END} = $pos;
+ $hash{SVTYPE} = "INS";
+ $hash{END} = $pos;
}elsif (length($alt) < length($ref)) {
- my $diff = substr($ref, length($alt));
- $hash{SVTYPE} = "DEL";
+ my $diff = substr($ref, length($alt));
+ $hash{SVTYPE} = "DEL";
$hash{END} = $pos + length($diff);
}
next unless ($hash{ANN});
@@ -92,7 +92,7 @@ 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(/\|/,$trx);
- next unless ($impact =~ m/HIGH|MODERATE/ || $effect =~ /splice/i);
+ next unless ($impact =~ m/HIGH|MODERATE|LOW/ || $effect =~ /splice/i);
next if($effect eq 'sequence_feature');
$keeptrx = $trx;
$keepforvcf = $gene;
@@ -107,7 +107,6 @@ W1:while (my $line = <IN>) {
push @nannot, $info;
}
}
-
my $newannot = join(";",@nannot);
if ($hash{SVTYPE} eq 'INS' || ($hash{SVTYPE} eq 'DEL' && $keepforvcf !~ m/&/)) {
if ($filter =~ m/LOWMAPQ|LowQual/i) {
@@ -231,9 +230,6 @@ close IN;
foreach my $id (keys %svpairs) {
- if ($id =~ m/815016443/) {
- warn "debugging\n";
- }
my $alt1 = $svpairs{$id}{1}{alt};
my $alt2 = $svpairs{$id}{2}{alt};
my $svtype;
@@ -242,14 +238,14 @@ foreach my $id (keys %svpairs) {
}elsif ($alt2 =~ m/^\w\[/ && $alt1 =~ m/^\]/) {
$svtype = 'INS';
}else {
- $svtype = 'UNK';
+ $svtype = 'UNK';
}
- if ($svtype eq 'INS' || ($svtype eq 'DEL' && $svpairs{$id}{1}{gene} !~ m/&/ && $svpairs{$id}{1}{span} < 9999)) {
- if ($filter =~ m/LOWMAPQ|LowQual/i) {
+ if ($svtype eq 'INS' || ($svtype eq 'DEL' && $svpairs{$id}{1}{gene} !~ m/&/ && $svpairs{$id}{1}{span} < 9999)) {
+ if ($filter =~ m/LOWMAPQ|LowQual/i) {
$filter = 'FailedQC'.$filter;
- }
+ }
print VCFOUT $svpairs{$id}{1}{vcfline},"\n"
- }elsif ($svtype eq 'DEL' && $svpairs{$id}{1}{span} && $svpairs{$id}{1}{span} > 9999) {
- print DELFUS $svpairs{$id}{1}{fusionline},"\n";
- }
+ }elsif ($svtype eq 'DEL' && $svpairs{$id}{1}{span} && $svpairs{$id}{1}{span} > 9999) {
+ print DELFUS $svpairs{$id}{1}{fusionline},"\n";
+ }
}
diff --git a/variants/svcalling.sh b/variants/svcalling.sh
index c751db3..562d2ee 100755
--- a/variants/svcalling.sh
+++ b/variants/svcalling.sh
@@ -95,7 +95,7 @@ then
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
- 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|transcript_ablation' | sort -u > ${pair_id}.dgf.txt
mv ${pair_id}.delly.vcf.gz ${pair_id}.delly.ori.vcf.gz
echo "perl $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
@@ -126,7 +126,7 @@ then
if [[ $filter == 1 ]]
then
- 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
+ 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|transcript_ablation' | 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
--
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