use strict;
use warnings;

my %data;

while (<DATA>) {
    chomp;
    my ($snp, $ind, @parts) = split;

    next if @parts < 2;

    $data{$ind}{$snp} = \@parts;
}

for my $ind (sort keys %data) {
    print "$ind";

    for my $snp (sort keys %{$data{$ind}}) {
        my $parts = $data{$ind}{$snp};
        
        print "\t$parts->[0]\t$parts->[1]";
    }

    print "\n";
}

__DATA__
SNP5	IND1	A5	C5	0.8
SNP2	IND1	A2	C2	0.8
SNP1	IND1	A1	C1	0.8
SNP3	IND1	A3	C3	0.8
SNP4	IND1	A4	C4	0.8
SNP5	IND2	G5	T5	0.8
SNP2	IND2	G2	T2	0.8
SNP1	IND2	G1	T1	0.8
SNP3	IND2	G3	T3	0.8
SNP4	IND2	G4	T4	0.8