adding dependencies

variants/gatkrunner.sh

@@ -58,7 +58,7 @@ fi
 
 source /etc/profile.d/modules.sh
 user=$USER
-module load gatk/4.x singularity/2.6.1
+module load gatk/4.x singularity/2.6.1 samtools/gcc/1.8
 mkdir /tmp/${user}
 export TMP_HOME=/tmp/${user}
 

variants/unionvcf.pl

@@ -133,7 +133,7 @@ foreach $vcf (@vcffiles) {
     }else {
 	$filter = '.';
     }
-    $lines{$chrom}{$pos}{$alt}{$caller} = [$chrom,$pos,$id,$ref,$alt,$score,$filter,$annot,$newformat,\@newgts,\@gtdesc];
+    $lines{$chrom}{$pos}{$ref}{$alt}{$caller} = [$chrom,$pos,$id,$ref,$alt,$score,$filter,$annot,$newformat,\@newgts,\@gtdesc];
   }
   close VCF;
 }
@@ -141,44 +141,46 @@ my @callers = ('fb','mutect','gatk','platypus','strelka2','shimmer','virmid');
 
 F1:foreach $chr (sort {$a cmp $b} keys %lines) {
  F2:foreach $pos (sort {$a <=> $b} keys %{$lines{$chr}}) {
-  F4:foreach $alt (sort {$a <=> $b} keys %{$lines{$chr}{$pos}}) {
-      my @callset;
-      my %csets;
-      my %depth;
-    F3:foreach $caller (sort {$a cmp $b} keys %{$lines{$chr}{$pos}{$alt}}) {
-	my ($chrom, $pos,$id,$ref,$alt,$score,$filter,$annot,
-	    $format,$gtsref,$gtdescref) = @{$lines{$chr}{$pos}{$alt}{$caller}};
-	my @gtdesc = @{$gtdescref};
-	my @gtdesc2;	
-	foreach $gtd (@gtdesc) {
-	  my ($id,$dp,$maf) = split(/:/,$gtd);
-	  push @gtdesc2, $dp;
-	  push @{$csets{$id}}, [$caller,$dp,$maf];
-	}
-	@gtdesc2 = sort {$b <=> $a} @gtdesc2;
-	$depth{$caller} = $gtdesc2[0];
-	push @callset, join("|",$caller,$alt,@gtdesc);
-      }
-      my $consistent = 1;
-      foreach $id (keys %csets) {
-	my @calls = @{$csets{$id}};
-	my @calls = sort {$a[2] <=> $b[2]} @calls;
-	$consistent = 0 if ($calls[0][2] < 0.25 && $calls[-1][2] - $calls[0][2] > 0.10 && $calls[-1][2]/($calls[0][2]+0.001) > 3);
-      }
-      @callorder = sort {$depth{$b} <=> $depth{$a}} keys %depth;
-    F3:foreach $caller (@callers) {
-	if ($lines{$chr}{$pos}{$alt}{$caller}) {
+  F5:foreach $ref (sort {$a <=> $b} keys %{$lines{$chr}{$pos}}) {
+    F4:foreach $alt (sort {$a <=> $b} keys %{$lines{$chr}{$pos}{$ref}}) {
+	my @callset;
+	my %csets;
+	my %depth;
+      F3:foreach $caller (sort {$a cmp $b} keys %{$lines{$chr}{$pos}{$ref}{$alt}}) {
 	  my ($chrom, $pos,$id,$ref,$alt,$score,$filter,$annot,
-	      $format,$gtsref,$gtdescref) = @{$lines{$chr}{$pos}{$alt}{$caller}};
-	  @gts = @{$gtsref};
-	  @gtdesc = @{$gtdescref};
-	  $annot = $annot.";CallSet=".join(",",@callset);
-	  unless ($consistent) {
-	    $annot = $annot.";CallSetInconsistent=1";
+	      $format,$gtsref,$gtdescref) = @{$lines{$chr}{$pos}{$ref}{$alt}{$caller}};
+	  my @gtdesc = @{$gtdescref};
+	  my @gtdesc2;	
+	  foreach $gtd (@gtdesc) {
+	    my ($id,$dp,$maf) = split(/:/,$gtd);
+	    push @gtdesc2, $dp;
+	    push @{$csets{$id}}, [$caller,$dp,$maf];
+	  }
+	  @gtdesc2 = sort {$b <=> $a} @gtdesc2;
+	  $depth{$caller} = $gtdesc2[0];
+	  push @callset, join("|",$caller,$alt,@gtdesc);
+	}
+	my $consistent = 1;
+	foreach $id (keys %csets) {
+	  my @calls = @{$csets{$id}};
+	  my @calls = sort {$a[2] <=> $b[2]} @calls;
+	  $consistent = 0 if ($calls[0][2] < 0.25 && $calls[-1][2] - $calls[0][2] > 0.10 && $calls[-1][2]/($calls[0][2]+0.001) > 3);
+	}
+	@callorder = sort {$depth{$b} <=> $depth{$a}} keys %depth;
+      F3:foreach $caller (@callers) {
+	  if ($lines{$chr}{$pos}{$ref}{$alt}{$caller}) {
+	    my ($chrom, $pos,$id,$ref,$alt,$score,$filter,$annot,
+		$format,$gtsref,$gtdescref) = @{$lines{$chr}{$pos}{$ref}{$alt}{$caller}};
+	    @gts = @{$gtsref};
+	    @gtdesc = @{$gtdescref};
+	    $annot = $annot.";CallSet=".join(",",@callset);
+	    unless ($consistent) {
+	      $annot = $annot.";CallSetInconsistent=1";
+	    }
+	    print OUT join("\t",$chrom,$pos,$id,$ref,$alt,$score,
+			   $filter,$annot,$format,@gts),"\n";
+	    last F3;
 	  }
-	  print OUT join("\t",$chrom,$pos,$id,$ref,$alt,$score,
-			 $filter,$annot,$format,@gts),"\n";
-	  last F3;
 	}
       }
     }