/usr/bin/vcf-convert is in vcftools 0.1.12+dfsg-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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Vcf;
use FindBin;
use lib "$FindBin::Bin";
use FaSlice;
my $opts = parse_params();
convert_file($opts);
exit;
#--------------------------------
sub error
{
my (@msg) = @_;
if ( scalar @msg )
{
croak @msg;
}
die
"About: Convert between VCF versions.\n",
"Usage: cat in.vcf | vcf-convert [OPTIONS] > out.vcf\n",
"Options:\n",
" -r, --refseq <file> The reference sequence in samtools faindexed fasta file. (Not required with SNPs only.)\n",
" -v, --version <string> 4.0, 4.1, 4.2\n",
" -h, -?, --help This help message.\n",
"\n";
}
sub parse_params
{
my $opts = { version=>'4.2' };
while (my $arg=shift(@ARGV))
{
if ( $arg eq '-r' || $arg eq '--refseq' ) { $$opts{refseq}=shift(@ARGV); next; }
if ( $arg eq '-v' || $arg eq '--version' ) { $$opts{version}=shift(@ARGV); next; }
if ( $arg eq '-?' || $arg eq '-h' || $arg eq '--help' ) { error(); }
error("Unknown parameter \"$arg\". Run -h for help.\n");
}
return $opts;
}
sub convert_file
{
my ($opts) = @_;
# How to recognise a number
my $FLOAT_RE = qr/^\-?\d+\.?\d*(?:[eE][+-]\d+)?$/;
my $vcf_in = Vcf->new(fh=>\*STDIN);
my $vcf_out = Vcf->new(version=>$$opts{version});
if ( $$opts{version} < $$vcf_in{version} ) { warn("Downgrading of VCF versions is experimental: expect troubles!\n"); }
# Convert the header
$vcf_in->parse_header();
for (my $i=1; $i<@{$$vcf_in{header_lines}}; $i++)
{
$vcf_out->add_header_line($$vcf_in{header_lines}[$i]);
}
$vcf_out->add_columns(@{$$vcf_in{columns}});
print $vcf_out->format_header();
# Convert each data line
my $fa;
while (my $x=$vcf_in->next_data_hash())
{
# Convert missing (default) FORMAT values
for my $gt (values %{$$x{gtypes}})
{
for my $field (@{$$x{FORMAT}})
{
# Skip the GT tag, so that ploidy information is not lost ("./." would become ".")
if ( $field eq 'GT' ) { next; }
if ( $field eq 'FT' && $$gt{$field} eq $$vcf_in{filter_passed} ) { $$gt{$field}=$$vcf_out{filter_passed}; }
if ( exists($$vcf_in{defaults}{$field}) && $$vcf_in{defaults}{$field} eq $$gt{$field} )
{
$$gt{$field} = $$vcf_out{defaults}{$field};
next;
}
if ( !exists($$gt{$field}) ) { next; }
if ( exists($$vcf_in{header}{FORMAT}{$field}{default}) && $$vcf_in{header}{FORMAT}{$field}{default} eq $$gt{$field} )
{
delete($$gt{$field});
next;
}
}
}
# Change missing QUAL: In case they are numbers, do numeric comparison, as -1.0 is sometimes used instead of -1
if ( $$x{QUAL} eq $$vcf_in{defaults}{QUAL}
or ($$x{QUAL}=~$FLOAT_RE && $$vcf_in{defaults}{QUAL}=~$FLOAT_RE && $$x{QUAL}==$$vcf_in{defaults}{QUAL}) )
{
$$x{QUAL} = $$vcf_out{defaults}{QUAL};
}
for (my $i=0; $i<@{$$x{FILTER}}; $i++)
{
if ( $$x{FILTER}[$i] eq $$vcf_in{filter_passed} ) { $$x{FILTER}[$i] = $$vcf_out{filter_passed}; }
}
# Parse the ALT column and see if there are indels
my $has_indel = 0;
for my $alt (@{$$x{ALT}})
{
my ($type,$len,$ht) = $vcf_in->event_type($x,$alt);
if ( $type eq 's' or $type eq 'r' ) { next; }
if ( $type ne 'i' ) { error("FIXME: expected indel at $$x{CHROM}:$$x{POS}\n"); }
$has_indel = 1;
}
# If there is an indel, new REF and ALT must be changed
if ( $has_indel )
{
my $map = {};
my $alt_to_mapref = {};
for my $alt (@{$$x{ALT}})
{
my ($type,$len,$ht) = $vcf_in->event_type($x,$alt);
if ( $type eq 's' or $type eq 'r' )
{
$$alt_to_mapref{$alt} = { ref=>$$x{REF}, alt=>$alt };
$$map{$$x{REF}}{$alt} = 1;
next;
}
if ( $type eq 'i' && $len>0 )
{
my $tmp = $$x{REF}.$ht;
$$alt_to_mapref{$alt} = { ref=>$$x{REF}, alt=>$tmp };
$$map{$$x{REF}}{$tmp} = 1;
next;
}
elsif ( $type eq 'i' && $len<0 )
{
if ( !$fa )
{
if ( !$$opts{refseq} ) { error("Indels present, missing the -r option.\n"); }
$fa = FaSlice->new(file=>$$opts{refseq},size=>1_000_000);
}
my $ref = $fa->get_slice($$x{CHROM},$$x{POS},$$x{POS}+abs($len));
my $nref1 = uc(substr($ref,0,1));
my $oref1 = uc(substr($$x{REF},0,1));
# Sanity check
if ( $oref1 ne $nref1 )
{
error("Sanity check failed: the ref does not agree at $$x{CHROM}:$$x{POS} .. [$nref1] in .fa, [$oref1] in .vcf\n");
}
$$alt_to_mapref{$alt} = { ref=>$ref, alt=>$$x{REF} };
$$map{$ref}{$$x{REF}} = 1;
next;
}
else
{
error("Uh, FIXME: $$x{CHROM}:$$x{POS} [$type] [$len] [$ht]\n");
}
}
$$x{REF} = $vcf_out->fill_ref_alt_mapping($map);
if ( !defined $$x{REF} ) { error("Failed on line $$x{CHROM}:$$x{POS}\n"); }
for (my $i=0; $i<@{$$x{ALT}}; $i++)
{
my $ori_ref = $$alt_to_mapref{$$x{ALT}[$i]}{ref};
my $ori_alt = $$alt_to_mapref{$$x{ALT}[$i]}{alt};
$$x{ALT}[$i] = $$map{$ori_ref}{$ori_alt};
}
}
print $vcf_out->format_line($x);
}
}
|