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Commit 2f76edc9 authored by Brandi Cantarel's avatar Brandi Cantarel
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update delly svaba sv calling filter

parent 7da44e40
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variants/filter_delly.pl
+ 4
− 0
View file @ 2f76edc9
...@@ -99,6 +99,9 @@ W1:while (my $line = <IN>) { ...@@ -99,6 +99,9 @@ W1:while (my $line = <IN>) {
} }
} }
my $newannot = join(";",@nannot); my $newannot = join(";",@nannot);
if ($filter ne 'PASS') {
$filter = 'FailedQC;'.$filter;
}
if ($hash{SVTYPE} eq 'INS' || ($hash{SVTYPE} eq 'DEL' && $keepforvcf !~ m/&/)) { if ($hash{SVTYPE} eq 'INS' || ($hash{SVTYPE} eq 'DEL' && $keepforvcf !~ m/&/)) {
print VCFOUT join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$newannot, print VCFOUT join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$newannot,
$format,@gts),"\n"; $format,@gts),"\n";
...@@ -106,6 +109,7 @@ W1:while (my $line = <IN>) { ...@@ -106,6 +109,7 @@ 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(/\|/,$keeptrx); $cds_pos,$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"; print DELFUS join("\t",$chrom,$pos,$hash{CHR2},$hash{END},$effect,$gene,$biotype,$filter,$format,@gts),"\n";
} }
} }
......
variants/filter_svaba.pl
+ 1
− 1
View file @ 2f76edc9
...@@ -110,7 +110,7 @@ W1:while (my $line = <IN>) { ...@@ -110,7 +110,7 @@ W1:while (my $line = <IN>) {
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) {
$filter = 'FailedQC'.$filter; $filter = 'FailedQC;'.$filter;
} }
print VCFOUT join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$newannot, print VCFOUT join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$newannot,
$format,@gts),"\n"; $format,@gts),"\n";
......
variants/svcalling.sh
+ 5
− 5
View file @ 2f76edc9
...@@ -96,12 +96,12 @@ then ...@@ -96,12 +96,12 @@ then
then then
tid=`samtools view -H ${sbam} |grep '^@RG' |perl -pi -e 's/\t/\n/g' |grep ID |cut -f 2 -d ':'` tid=`samtools view -H ${sbam} |grep '^@RG' |perl -pi -e 's/\t/\n/g' |grep ID |cut -f 2 -d ':'`
fi 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 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 perl $baseDir/filter_delly.pl -t $tid -p $pair_id -i ${pair_id}.delly.ori.vcf.gz
bgzip ${pair_id}.delly.vcf bgzip -f ${pair_id}.delly.vcf
cat ${pair_id}.delly.potentialfusion.txt ${pair_id}.dgf.txt |sort -u > ${pair_id}.delly.genefusion.txt 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 fi
elif [[ $method == 'svaba' ]] elif [[ $method == 'svaba' ]]
then then
...@@ -122,11 +122,11 @@ then ...@@ -122,11 +122,11 @@ then
if [[ $filter == 1 ]] if [[ $filter == 1 ]]
then 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 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 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
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 cat ${pair_id}.svaba.potentialfusion.txt ${pair_id}.sgf.txt | sort -u >> ${pair_id}.svaba.genefusion.txt
fi fi
elif [[ $method == 'lumpy' ]] elif [[ $method == 'lumpy' ]]
......
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