XL.pl

#!/usr/bin/perl
#
#10/01/2013 - allow user to enter proband index, default is still 35
#
#XL.pl usage: XL.pl [options] annotated_vcf.vcf>
#options:
#--PROBAND=<proband_index> . Defaults to 35
#--NUM_AFFECTED=<number_of_affecteds> . Defaults to 1.
#Filters annotated vcf X-linked variants in male probands. User can supply the proband index. Default value is 35. Also can handle multiple affecteds. Default NUM_AFFECTED is 1.
#The order of the input vcf is important. Must follow this order: <proband_1> <proband_n> <father> <mother>
#Dalia Ghoneim
#
use strict;
use warnings;
use Getopt::Long;
my $NUM_AFFECTED=1;
my $proband_index=35;
my $aff_geno_match;
GetOptions ('NUM_AFFECTED:i'=>\$NUM_AFFECTED, 'PROBAND:i'=>\$proband_index);
my $file = shift;
my $i;

my $father_index=$proband_index+$NUM_AFFECTED;
my $mother_index=$proband_index+1+$NUM_AFFECTED;
open my ($F), $file;
#filter for XL variant
LINE: while ($_=<$F>){
	#my @line;
	if ($_ =~ m{Gene} ) { print $_; }
	if ($_ =~ m{\tX\t}){
	       		my @line = split /\t/;
        	if ((($line[$proband_index] =~ m{0/1})&&($line[$father_index] =~ m{0/0})&&($line[$mother_index] =~ m{0/1}))){
                	#handle multiple affected
                	$aff_geno_match=1;
                	for($i=1;$i<$NUM_AFFECTED;$i++){
                        	if ($line[$proband_index+$i]=~m{0/1}){
                                	$aff_geno_match++;
                        	}
                	}
                	if ($aff_geno_match == $NUM_AFFECTED){
		   		print join(qq/\t/, @line);
                	}
		}
	}
}
close $F;