TERT 基因过滤

codes/filter_snpindel.pl

@@ -40,13 +40,14 @@ print OUT "$new_head\n";
 print TAG_OUT "TAG\t$head\n";
 
 my %blacklist = blacklist();
-my ($muts_ref, $hcs_ref, $mmr_ref, $hhr1_ref, $hhr2_ref) = info();
+my ($muts_ref, $hcs_ref, $mmr_ref, $hhr1_ref, $hhr2_ref, $promoter_ref) = info();
 
 my @muts = @$muts_ref;
 my @hcs = @$hcs_ref;
 my @mmr = @$mmr_ref;
 my @hhr1 = @$hhr1_ref;
 my @hhr2 = @$hhr2_ref;
+my @promoter = @$promoter_ref;
 
 my %transcript = transcript();
 my %oncogenic = get_oncogenic();
@@ -209,6 +210,12 @@ while (<IN>) {
         }
     }
 
+    # TERT 突变特殊处理 不过滤
+    if ((grep {$_ eq $gene} @promoter) and ($pipeline eq 'somatic') and ($gene eq 'TERT')
+        and ($line[1] eq '1295228' and $line[4] eq 'A') or ($line[1] eq '1295250' and $line[4] eq 'A')) {
+        @reason = ();
+    }
+
     if (@reason) {
         print TAG_OUT join(";", @reason), "\t", join("\t", @line), "\n";
         next;
@@ -250,6 +257,10 @@ while (<IN>) {
     if (grep {$_ eq $gene} @hhr2) {
         push @genetags, 'hrr2';
     }
+    if (grep {$_ eq $gene} @promoter) {
+        @genetags = ();
+        push @genetags, 'promoter';
+    }
 
     my $validated = '1';
 
@@ -304,9 +315,12 @@ sub info {
             if ($record{'HRR_II'} ne "NA") {
                 @hhr2 = split(/\//, $record{'HRR_II'});
             }
+            if ($record{'promoter'} ne "NA") {
+                @promoter = split(/\//, $record{'promoter'});
+            }
         }
     }
-    return \@muts, \@hcs, \@mmr, \@hhr1, \@hhr2
+    return \@muts, \@hcs, \@mmr, \@hhr1, \@hhr2, \@promoter,
 }
 
 sub transcript {