#!/usr/bin/env perl

use strict;
use warnings;

my $data = $ARGV[0];

my ($line, @line, $effect);

print "Chr\tPos\tRef\tAlt\tEffect\tBeta\tBeta_SE\tBeta_pval\n";

open(DATA, "<$data");


while(<DATA>) {

    $line = $_;
    chomp($line);

    @line = split(" ", $line);

    ## Check for the header

    if ($line =~ m/CHR/) {
        next;
    }

    ## If it is a possible indel, next line

    if (length ($line[3]) > 1 or length ($line[4]) > 1) {
        next;
    }

    $effect = $line[3];


    #$line[8] =  log($line[8])/log(10);

    if ($line[8] < 0) {

        $effect = $line[4];

        $line[8] = -$line[8];

    }

    print "$line[0]\t$line[2]\t$line[3]\t$line[4]\t$effect\t$line[8]\t$line[9]\t$line[10]\n";

}