Perl script to parse VCF file !

LEGE — Thu, 01 Feb 2024 02:08:11 -0600

#!/usr/bin/perl

use strict;
use warnings;

# Usage: ./parse_vcf.pl input.vcf

die "Usage: ./parse_vcf.pl input.vcf\n" unless @ARGV;

my $vcf_file = shift @ARGV;
my @vcf_entries = parse_vcf($vcf_file);

print "Total entries: ", scalar(@vcf_entries), "\n";
print "---------------------------\n";

my %chromosome_counts;
for my $entry (@vcf_entries) {
    $chromosome_counts{$entry->{CHROM}}++;
}

print "Chromosome counts:\n";
for my $chromosome (sort keys %chromosome_counts) {
    print "  $chromosome: $chromosome_counts{$chromosome}\n";
}

sub parse_vcf {
    my ($file) = @_;

    open my $fh, '<', $file or die "Cannot open file $file: $!\n";

    my @entries;

    while (my $line = <$fh>) {
        next if $line =~ /^\s*$/;  # skip empty lines
        next if $line =~ /^\s*#/; # skip comments

        chomp $line;
        my @fields = split /\t/, $line;

        my %entry;
        @entry{qw/CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLES/} = @fields;

        push @entries, \%entry;
    }

    close $fh;

    return @entries;
}

BOL: Perl script to parse VCF file !

Perl script to parse VCF file !