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Perl script to parse VCF file !

  • Public
By LEGE 328 days ago
#!/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; }