If you don't mind introducing Moose and its dependencies, then MooseX::Getopt is a good way of setting up command-line options (some of the features that I'm using here are documented in MooseX::Getopt::Meta::Attribute)

For example, in MyApp.pm

package MyApp;
use Moose;
 
with 'MooseX::Getopt';
 
has 'extension' => (
    traits => ['Getopt'],
    is => 'rw',
    isa => 'Str',
    cmd_aliases => 'b',
    documentation => 'Short description of extension'
);

has 'liste_snp' => (
    traits => ['Getopt'],
    is => 'rw',
    isa => 'Str',
    cmd_aliases => 'l'
);

has 'min_snp_per_cds' => (
    traits => ['Getopt'],
    is => 'rw',
    isa => 'Bool',
    cmd_aliases => 's',
    default => 1
);

has 'liste_geno' => (
    traits => ['Getopt'],
    is => 'rw',
    isa => 'Str',
    cmd_aliases => 'g'
);

has 'reference_cds_fasta' => (
    traits => ['Getopt'],
    is => 'rw',
    isa => 'Str',
    cmd_aliases => 'r'
);

has 'prefixe' => (
    traits => ['Getopt'],
    is => 'rw',
    isa => 'Str',
    cmd_aliases => 'p'
);

has 'min_read_classe' => (
    traits => ['Getopt'],
    is => 'rw',
    isa => 'Int',
    cmd_aliases => 'mc',
    default => 30
);

has 'max_read_per_cent_ambi' => (
    traits => ['Getopt'],
    is => 'rw',
    isa => 'Num',
    cmd_aliases => 'a',
    default => 1
);

sub print_options {
    my $self = shift;
    my $bam = $self->extension // 'undefined';
    my $liste_snp = $self->liste_snp // 'undefined';
    my $min_snp_cds = $self->min_snp_per_cds // 'undefined';
    my $list_geno = $self->liste_geno // 'undefined';
    my $ref_cds = $self->reference_cds_fasta // 'undefined';
    my $prefixe = $self->prefixe // 'undefined';
    my $seuil_min_classe = $self->min_read_classe // 'undefined';
    my $seuil_max_amb = $self->max_read_per_cent_ambi // 'undefined';
    print "extension: $bam\n";
    print "liste_snp: $liste_snp\n";
    print "min_snp_per_cds: $min_snp_cds\n";
    print "list_geno: $list_geno\n";
    print "reference_cds_fasta: $ref_cds\n";
    print "prefixe: $prefixe\n";
    print "min_read_classe: $seuil_min_classe\n";
    print "max_read_per_cent_ambi: $seuil_max_amb\n";
}

1;
[download]

#!/usr/bin/env perl
 
use MyApp;
 
my $app = MyApp->new_with_options();

$app->print_options;

# ... rest of the script here
exit;
[download]

extension: undefined
liste_snp: undefined
min_snp_per_cds: 1
list_geno: undefined
reference_cds_fasta: undefined
prefixe: undefined
min_read_classe: 30
max_read_per_cent_ambi: 1
[download]

extension: myext
liste_snp: undefined
min_snp_per_cds: 1
list_geno: undefined
reference_cds_fasta: undefined
prefixe: undefined
min_read_classe: 40
max_read_per_cent_ambi: 1
[download]

usage: runapp.pl [-?abghlprs] [long options...]
    -h -? --usage --help                   Prints this usage informati
+on.
    -b STR --extension STR                 Short description of extens
+ion
    -l STR --liste_snp STR
    -s --min_snp_per_cds
    -g STR --liste_geno STR
    -r STR --reference_cds_fasta STR
    -p STR --prefixe STR
    --mc INT --min_read_classe INT
    -a NUM --max_read_per_cent_ambi NUM
[download]