update filter pindel.pl

variants/filter_pindel.pl

@@ -80,7 +80,6 @@ foreach $file (@files) {
     next if ($tumoraltct[0] eq '.');
     $hash{AF} = join(",",@tumormaf);
     next if ($tumoraltct[0] < 20);
-    next if ($tumormaf[0] < 0.05);
     my $keepforvcf = 0;
     foreach $trx (split(/,/,$hash{ANN})) {
       my ($allele,$effect,$impact,$gene,$geneid,$feature,
@@ -94,6 +93,9 @@ foreach $file (@files) {
       $keepforvcf = $gene;
     }
     next unless $keepforvcf;
+    if ($tumormaf[0] < 0.1) {
+	next unless ($outfile =~ m/pindel_tandemdup/);
+    }
     my @fail = sort {$a cmp $b} keys %fail;
     next if (scalar(@fail) > 0);
     my @nannot;