Have you ever noticed the "download" link at the bottom of each code section? I clicked it to download the data including tabs, but they included the filenames. Don't make them part of the code section.

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
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I'm struggling to understand why if you want to 'merge' records from 3 files you are creating hash keys containing the filename ?

$fields[2] = $file;
my $locus = join "\t", @fields[0,1,2,3,4,5];
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From this output code, it looks like you want to create a 'cross tab' with HET/HOM derived from each file in a different column. Is that correct ?

my $samples_list = join "\t", @samples;
print OUT "CHROM    POS    ID    REF    ALT    QUAL    $samples_list
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Think about: what is the minimum amount of code and sample data needed so that others can reproduce the problem? For each line of code, try removing it - does the problem still exist? If yes, it was ok to remove that line, if the problem goes away, put the line back in. And if removing the line causes a compilation failure, fix that first. See also Short, Self-Contained, Correct Example.

Hi drlecb. There are a few ways to include sample files with your program on Perlmonks. To include it like you did and have the Perl program still be runnable you can add __DATA__ or __END__ after your Perl program and anything after it will be treated as data or comments. Another way is to start a new code section for your sample file with  <c> ... </c> so that the monks can click download for the sample file.

Here is an example of using __DATA__

use warnings;
use strict;

while(<DATA>){
    my $line = $_;
    print $line;
}
__DATA__
Line 1
Line 2
Line 3
[download]