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$hash_geno_group{$sample_geno_group}{"sample"}=$sample_nm;

push @{ $hash_geno_group{$sample_geno_group}{sample} }, $sample_nm;

Use of my $_ is experimental at test_fontion4.pl line 68.
keys on reference is experimental at test_fontion4.pl line 187.

while (defined(my $_ = <GENOTYPED>))

while (<GENOTYPED>)

keys %{ $hash_ref }

open my $genotyped_fh, '<', $list_geno or die "Cannot open $list_geno\
+n";