/usr/bin/vcf-stats is in vcftools 0.1.15-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 | #!/usr/bin/env perl
#
# Author: petr.danecek@sanger
#
use strict;
use warnings;
use Carp;
use VcfStats;
my $opts = parse_params();
vcf_stats($opts);
exit;
#--------------------------------
sub error
{
my (@msg) = @_;
if ( scalar @msg )
{
croak @msg;
}
die
"Usage: vcf-stats [OPTIONS] file.vcf.gz\n",
"Options:\n",
" -d, --dump <file> Take an existing dump file and recreate the files (works with -p)\n",
" -f, --filters <filter1,filter2> List of filters such as column/field (any value), column/field=bin:max (cluster in bins),column/field=value (exact value)\n",
" -p, --prefix <dir/string> Prefix of output files. If slashes are present, directories will be created.\n",
" -s, --samples <list> Process only the listed samples, - for none. Excluding unwanted samples may increase performance considerably.\n",
" -h, -?, --help This help message.\n",
"\n",
"Examples:\n",
" # Calculate stats separately for the filter field, quality and non-indels\n",
" vcf-stats file.vcf.gz -f FILTER,QUAL=10:200,INFO/INDEL=False -p out/\n",
"\n",
" # Calculate stats for all samples\n",
" vcf-stats file.vcf.gz -f FORMAT/DP=10:200 -p out/\n",
"\n",
" # Calculate stats only for the sample NA00001\n",
" vcf-stats file.vcf.gz -f SAMPLE/NA00001/DP=1:200 -p out/\n",
"\n",
" vcf-stats file.vcf.gz > perl.dump\n",
"\n";
}
sub parse_params
{
my $opts = { filters=>{}, filter_param=>'' };
while (my $arg=shift(@ARGV))
{
if ( $arg eq '-d' || $arg eq '--dump' ) { $$opts{dump}=shift(@ARGV); next; }
if ( $arg eq '-f' || $arg eq '--filters' ) { $$opts{filter_param}=shift(@ARGV); next; }
if ( $arg eq '-p' || $arg eq '--prefix' ) { $$opts{prefix}=shift(@ARGV); next; }
if ( $arg eq '-s' || $arg eq '--samples' )
{
my $samples = shift(@ARGV);
$$opts{samples} = [ split(/,/,$samples) ];
next;
}
if ( -e $arg ) { $$opts{file} = $arg; next }
if ( $arg eq '-?' || $arg eq '-h' || $arg eq '--help' ) { error(); }
error("Unknown parameter or nonexistent file: \"$arg\". Run -h for help.\n");
}
if ( exists($$opts{dump}) && !exists($$opts{prefix}) ) { error("Expected -p option with -d.\n"); }
return $opts;
}
sub init_filters
{
my ($opts,$vcf) = @_;
for my $filter (split(/,/,$$opts{filter_param}))
{
my ($key,$value) = split(/=/,$filter);
my $rec = { value=>$value, exact=>0, any=>0, bin=>0, is_flag=>0 };
if ( $key=~m{^INFO/} )
{
my $tag = $';
$$rec{tag} = $tag;
if ( exists($$vcf{header}{'INFO'}) && exists($$vcf{header}{'INFO'}{$tag}) && $$vcf{header}{'INFO'}{$tag}{Type} eq 'Flag' )
{
$$rec{is_flag} = 1;
$$rec{value} = $value eq 'False' ? 0 : 1;
$key = "INFO/$tag=". ($$rec{value} ? 'True':'False');
}
}
elsif ( $key eq 'INFO' )
{
# All INFO flags should be counted
for my $tag (keys %{$$vcf{header}{'INFO'}})
{
if ( $$vcf{header}{'INFO'}{$tag}{Type} ne 'Flag' ) { next; }
$$opts{filters}{"INFO/$tag=True"} = { %$rec, is_flag=>1, value=>1, tag=>$tag };
}
next;
}
if ( ! defined $value )
{
$$rec{any} = 1;
}
elsif ( $value=~/^(.+):(.+)$/ )
{
$$rec{bin} = 1;
$$rec{bin_size} = $1;
$$rec{max} = $2;
}
else
{
$$rec{exact} = 1;
}
$$opts{filters}{$key} = $rec;
}
}
sub vcf_stats
{
my ($opts) = @_;
if ( exists($$opts{dump}) )
{
# Use existing dump to recreate the files
my $vcf = VcfStats->new(file=>'/dev/null');
$$vcf{stats} = do $$opts{dump};
$vcf->save_stats($$opts{prefix});
return;
}
# Open the VCF file
my $vcf = $$opts{file} ? VcfStats->new(file=>$$opts{file}) : VcfStats->new(fh=>\*STDIN);
$vcf->parse_header();
init_filters($opts,$vcf);
# Include only requested samples
if ( exists $$opts{samples} )
{
my @include = ();
if ( scalar @{$$opts{samples}}>1 or $$opts{samples}[0] ne '-' )
{
for my $sample (@{$$opts{samples}}) { push @include,$sample; }
}
$vcf->set_samples(include=>\@include);
}
while (my $rec=$vcf->next_data_hash())
{
$vcf->collect_stats($rec,$$opts{filters});
}
$vcf->save_stats($$opts{prefix});
}
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