update delly svaba sv calling filter

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";
   }
 }

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";

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' ]]