Merge pull request #5 from cancerit/develop

Revises gender determiniation to be based on normal sample, comparison t...
cancerit · Jan 13, 2015 · 83bcaa5 · 83bcaa5
2 parents cb82e34 + eb49ef2
commit 83bcaa5
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Showing 3 changed files with 4 additions and 6 deletions.
diff --git a/docs.tar.gz b/docs.tar.gz
diff --git a/lib/Sanger/CGP/NgsQc.pm b/lib/Sanger/CGP/NgsQc.pm
@@ -36,7 +36,7 @@ use strict;
 use base 'Exporter';
 use Bio::DB::Sam;
 
-our $VERSION = '1.0.1';
+our $VERSION = '1.0.2';
 our @EXPORT = qw($VERSION);
 
 sub bam_sample_name {

diff --git a/lib/Sanger/CGP/NgsQc/CompareGenotypes.pm b/lib/Sanger/CGP/NgsQc/CompareGenotypes.pm
@@ -112,13 +112,11 @@ sub compare_samples {
   my $gender_loci_count = scalar @normal_calls_gender;
   my ($xy, $gender_match) = (0,0);
   for(my $i=0; $i<$gender_loci_count; $i++) {
-    if($normal_calls_gender[$i] eq $tumour_calls_gender[$i]) {
-      $gender_match++;
-      $xy++ if($tumour_calls_gender[$i] eq 'XY');
-    }
+    $gender_match++ if($normal_calls_gender[$i] eq $tumour_calls_gender[$i]);
+    $xy++ if($normal_calls_gender[$i] eq 'XY');
   }
   my $gender = 'XX';
-  $gender = 'XY' if($xy / $gender_loci_count >= 0.5);
+  $gender = 'XY' if($xy > 0); # any male specific loci present in normal results in XY call
   my %result_struct = ('sample' => $tumour,
                        'genotype' => {'frac_informative_genotype' =>  $informative / $loci_count,
                                       'frac_matched_genotype' => $matched / $informative},