Prevent bug from impacting NP

cancerit · Feb 21, 2022 · 66430ae · 66430ae
1 parent 37cac9d
commit 66430ae
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/perl/bin/pindel_np_from_vcf.pl b/perl/bin/pindel_np_from_vcf.pl
@@ -139,6 +139,7 @@ sub parse_vcf {
   my ($total, $kept, $new) = (0,0, 0);
   while(my $d = $vcf->next_data_hash) {
     $total++;
+    next if($d->{'REF'} eq $d->{'ALT'});
     my $gtypes = $d->{'gtypes'}->{$samp_id};
 
     next if(($gtypes->{'PP'} + $gtypes->{'NP'}) < $PINDEL_RAW_MIN);