exclude chrX variant from inheritance

Author: thomasguignard

wwwachab.pl

@@ -2224,11 +2224,14 @@
 			if ($line[0]!~/X/){
 
 				if (defined $skipCaseWT && $finalSortData[$dicoColumnNbr{"Genotype-".$case}] eq "0/0"){
-					switch ($familyGenotype){
-						#Check if case/dad and case/mum  inheritance are  consistent
-						case /^_0\/0_0\/1_0\/0_/ {$dadVariant ++ ;}
-						case /^_0\/0_0\/0_0\/1_/ {$mumVariant ++ ;}
-					}
+    					# exclude chromosome X variants due to mother/son unbalance
+					if ($line[0]!~/X/){
+						switch ($familyGenotype){
+							#Check if case/dad and case/mum  inheritance are  consistent
+							case /^_0\/0_0\/1_0\/0_/ {$dadVariant ++ ;}
+							case /^_0\/0_0\/0_0\/1_/ {$mumVariant ++ ;}
+						}
+      					}
 						next;
 				}
 
@@ -2240,8 +2243,7 @@
 					case /^_0\/1_0\/0_0\/1_/ {$caseMumVariant ++;}
 
 				}
-			}	
-
+			
 			if ($finalSortData[$dicoColumnNbr{"Genotype-".$case}] eq "0/0" or (! defined $hashAffected{$dad} and $finalSortData[$dicoColumnNbr{"Genotype-".$dad}] eq "1/1") or (! defined $hashAffected{$mum} and $finalSortData[$dicoColumnNbr{"Genotype-".$mum}] eq "1/1") ){
 				$finalSortData[$dicoColumnNbr{'MPA_ranking'}]   += 100;
 			}