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Commit dd30007d authored by Brandi Cantarel's avatar Brandi Cantarel
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update svcalling

parent 5bc467c7
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variants/filter_svaba.pl
+ 12
− 16
View file @ dd30007d
...@@ -41,11 +41,11 @@ W1:while (my $line = <IN>) { ...@@ -41,11 +41,11 @@ W1:while (my $line = <IN>) {
$hash{$key} = $val unless ($hash{$key}); $hash{$key} = $val unless ($hash{$key});
} }
if (length($alt) > length($ref)) { if (length($alt) > length($ref)) {
$hash{SVTYPE} = "INS"; $hash{SVTYPE} = "INS";
$hash{END} = $pos; $hash{END} = $pos;
}elsif (length($alt) < length($ref)) { }elsif (length($alt) < length($ref)) {
my $diff = substr($ref, length($alt)); my $diff = substr($ref, length($alt));
$hash{SVTYPE} = "DEL"; $hash{SVTYPE} = "DEL";
$hash{END} = $pos + length($diff); $hash{END} = $pos + length($diff);
} }
next unless ($hash{ANN}); next unless ($hash{ANN});
...@@ -92,7 +92,7 @@ W1:while (my $line = <IN>) { ...@@ -92,7 +92,7 @@ W1:while (my $line = <IN>) {
my ($allele,$effect,$impact,$gene,$geneid,$feature, my ($allele,$effect,$impact,$gene,$geneid,$feature,
$featureid,$biotype,$rank,$codon,$aa,$pos_dna,$len_cdna, $featureid,$biotype,$rank,$codon,$aa,$pos_dna,$len_cdna,
$cds_pos,$cds_len,$aapos,$aalen,$distance,$err) = split(/\|/,$trx); $cds_pos,$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'); next if($effect eq 'sequence_feature');
$keeptrx = $trx; $keeptrx = $trx;
$keepforvcf = $gene; $keepforvcf = $gene;
...@@ -107,7 +107,6 @@ W1:while (my $line = <IN>) { ...@@ -107,7 +107,6 @@ W1:while (my $line = <IN>) {
push @nannot, $info; push @nannot, $info;
} }
} }
my $newannot = join(";",@nannot); my $newannot = join(";",@nannot);
if ($hash{SVTYPE} eq 'INS' || ($hash{SVTYPE} eq 'DEL' && $keepforvcf !~ m/&/)) { if ($hash{SVTYPE} eq 'INS' || ($hash{SVTYPE} eq 'DEL' && $keepforvcf !~ m/&/)) {
if ($filter =~ m/LOWMAPQ|LowQual/i) { if ($filter =~ m/LOWMAPQ|LowQual/i) {
...@@ -231,9 +230,6 @@ close IN; ...@@ -231,9 +230,6 @@ close IN;
foreach my $id (keys %svpairs) { foreach my $id (keys %svpairs) {
if ($id =~ m/815016443/) {
warn "debugging\n";
}
my $alt1 = $svpairs{$id}{1}{alt}; my $alt1 = $svpairs{$id}{1}{alt};
my $alt2 = $svpairs{$id}{2}{alt}; my $alt2 = $svpairs{$id}{2}{alt};
my $svtype; my $svtype;
...@@ -242,14 +238,14 @@ foreach my $id (keys %svpairs) { ...@@ -242,14 +238,14 @@ foreach my $id (keys %svpairs) {
}elsif ($alt2 =~ m/^\w\[/ && $alt1 =~ m/^\]/) { }elsif ($alt2 =~ m/^\w\[/ && $alt1 =~ m/^\]/) {
$svtype = 'INS'; $svtype = 'INS';
}else { }else {
$svtype = 'UNK'; $svtype = 'UNK';
} }
if ($svtype eq 'INS' || ($svtype eq 'DEL' && $svpairs{$id}{1}{gene} !~ m/&/ && $svpairs{$id}{1}{span} < 9999)) { if ($svtype eq 'INS' || ($svtype eq 'DEL' && $svpairs{$id}{1}{gene} !~ m/&/ && $svpairs{$id}{1}{span} < 9999)) {
if ($filter =~ m/LOWMAPQ|LowQual/i) { if ($filter =~ m/LOWMAPQ|LowQual/i) {
$filter = 'FailedQC'.$filter; $filter = 'FailedQC'.$filter;
} }
print VCFOUT $svpairs{$id}{1}{vcfline},"\n" print VCFOUT $svpairs{$id}{1}{vcfline},"\n"
}elsif ($svtype eq 'DEL' && $svpairs{$id}{1}{span} && $svpairs{$id}{1}{span} > 9999) { }elsif ($svtype eq 'DEL' && $svpairs{$id}{1}{span} && $svpairs{$id}{1}{span} > 9999) {
print DELFUS $svpairs{$id}{1}{fusionline},"\n"; print DELFUS $svpairs{$id}{1}{fusionline},"\n";
} }
} }
variants/svcalling.sh
+ 2
− 2
View file @ dd30007d
...@@ -95,7 +95,7 @@ then ...@@ -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 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 ]] if [[ $filter == 1 ]]
then 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 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" 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 perl $baseDir/filter_delly.pl -t $tid -p $pair_id -i ${pair_id}.delly.ori.vcf.gz
...@@ -126,7 +126,7 @@ then ...@@ -126,7 +126,7 @@ then
if [[ $filter == 1 ]] if [[ $filter == 1 ]]
then 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 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 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 bgzip ${pair_id}.svaba.vcf
......
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