filter svaba to have 10kb + in fusion

variants/filter_svaba.pl

@@ -114,7 +114,7 @@ W1:while (my $line = <IN>) {
     }
     print VCFOUT join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$newannot,
 		      $format,@gts),"\n";
-  }elsif ($hash{SVTYPE} eq 'DEL' && $hash{SPAN} && $hash{SPAN} > 9999) {
+  } elsif ($hash{SVTYPE} eq 'DEL' && $hash{SPAN} && $hash{SPAN} > 9999) {
     my ($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);
@@ -230,6 +230,9 @@ 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;
@@ -237,8 +240,10 @@ foreach my $id (keys %svpairs) {
     $svtype = 'DEL';
   }elsif ($alt2 =~ m/^\w\[/ && $alt1 =~ m/^\]/) {
     $svtype = 'INS';
+  }else {
+      $svtype = 'UNK';
   }
-   if ($svtype eq 'INS' || ($svtype eq 'DEL' && $svpairs{$id}{1}{gene} !~ m/&/)) {
+   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;
     }

variants/svcalling.sh

@@ -123,7 +123,7 @@ 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
+	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

variants/uniform_vcf_gt.pl

@@ -27,15 +27,19 @@ while (my $line = <VCF>) {
 	my ($key,$val) = split(/=/,$a);
 	$hash{$key} = $val;
     }
-    if ($alt =~ m/^chr/) {
-	$chr2 =~ m/(chr\w+):(\d+)/;
-	$chr2=$1;
+    if ($alt =~ m/chr(\w+):(\d+)/i) {
+	$chr2='chr'.$1;
 	$p2 = $2;
 	$hash{CHR2} = $chr2;
 	$hash{'END'} = $p2;
 	$annot .= ";CHR2=$chr2;END=$p2";
+    }elsif ($alt =~ m/CHR(\w+):(\d+)/i) {
+	$chr2='chr'.$1;
+	$p2 = $2;
+	$hash{CHR2} = 'chr'.$1;
+	$hash{END} = $2;
+	$annot .= ";CHR2=$chr2;END=$p2";
     }
-
     my @deschead = split(/:/,$format);
     my $newformat = 'GT:DP:AD:AO:RO';
     my @newgts = ();
@@ -61,6 +65,10 @@ while (my $line = <VCF>) {
       } elsif ($gtdata{AD} =~ m/^\d+$/){
 	  $gtdata{AO} = $gtdata{AD};
 	  $gtdata{RO} = $gtdata{DP} - $gtdata{AO};
+	  if ($gtdata{RO} < 0) {
+	      $gtdata{DP} +=  $gtdata{AO};
+	      $gtdata{RO} = $gtdata{DP} -  $gtdata{AO};
+	  }
 	  $gtdata{AD} = join(',',$gtdata{RO},$gtdata{AO});
       } elsif (exists $gtdata{DV} && exists $gtdata{RV}) {
 	  $gtdata{AO} = $gtdata{DV} + $gtdata{RV};