#!/usr/bin/perl -w
#
-# VCF specs: http://www.1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcfv3.2
-
+# VCF specs: http://www.1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf3.3
+#
# Contact: pd3@sanger
-# Version: 2009-10-08
+# Version: 2010-04-23
use strict;
use warnings;
die
"Usage: sam2vcf.pl [OPTIONS] < in.pileup > out.vcf\n",
"Options:\n",
- " -r, -refseq <file.fa> The reference sequence, required when indels are present.\n",
- " -h, -?, --help This help message.\n",
+ " -h, -?, --help This help message.\n",
+ " -i, --indels-only Ignore SNPs.\n",
+ " -r, --refseq <file.fa> The reference sequence, required when indels are present.\n",
+ " -R, --keep-ref Print reference alleles as well.\n",
+ " -s, --snps-only Ignore indels.\n",
+ " -t, --column-title <string> The column title.\n",
"\n";
}
while (my $arg=shift(@ARGV))
{
+ if ( $arg eq '-R' || $arg eq '--keep-ref' ) { $opts{keep_ref}=1; next; }
if ( $arg eq '-r' || $arg eq '--refseq' ) { $opts{refseq}=shift(@ARGV); next; }
+ if ( $arg eq '-t' || $arg eq '--column-title' ) { $opts{title}=shift(@ARGV); next; }
+ if ( $arg eq '-s' || $arg eq '--snps-only' ) { $opts{snps_only}=1; next; }
+ if ( $arg eq '-i' || $arg eq '--indels-only' ) { $opts{indels_only}=1; next; }
if ( $arg eq '-?' || $arg eq '-h' || $arg eq '--help' ) { error(); }
error("Unknown parameter \"$arg\". Run -h for help.\n");
);
if ( !exists($iupac{$base}) )
{
- if ( $ref eq $base ) { return ('.','0|0'); }
- return ($base,'1|1');
+ if ( $base ne 'A' && $base ne 'C' && $base ne 'G' && $base ne 'T' ) { error("FIXME: what is this [$base]?\n"); }
+ if ( $ref eq $base ) { return ('.','0/0'); }
+ return ($base,'1/1');
}
my $gt = $iupac{$base};
- if ( $$gt[0] eq $ref ) { return ($$gt[1],'0|1'); }
- elsif ( $$gt[1] eq $ref ) { return ($$gt[0],'0|1'); }
- return ("$$gt[0],$$gt[1]",'1|2');
+ if ( $$gt[0] eq $ref ) { return ($$gt[1],'0/1'); }
+ elsif ( $$gt[1] eq $ref ) { return ($$gt[0],'0/1'); }
+ return ("$$gt[0],$$gt[1]",'1/2');
}
my $fh_out = $$opts{fh_out};
my ($prev_chr,$prev_pos,$prev_ref);
my $refseq;
+ my $ignore_indels = $$opts{snps_only} ? 1 : 0;
+ my $ignore_snps = $$opts{indels_only} ? 1 : 0;
+ my $keep_ref = $$opts{keep_ref} ? 1 : 0;
+ my $title = exists($$opts{title}) ? $$opts{title} : 'data';
+
+ print $fh_out
+ qq[##fileformat=VCFv3.3\n],
+ qq[##INFO=DP,1,Integer,"Total Depth"\n],
+ qq[##FORMAT=GT,1,String,"Genotype"\n],
+ qq[##FORMAT=GQ,1,Integer,"Genotype Quality"\n],
+ qq[##FORMAT=DP,1,Integer,"Read Depth"\n],
+ qq[#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t$title\n]
+ ;
while (my $line=<$fh_in>)
{
chomp($line);
- my ($chr,$pos,$ref,$cons,$cons_qual,$snp_qual,$rms_qual,$depth,@items) = split(/\t/,$line);
+ my (@items) = split(/\t/,$line);
+ if ( scalar @items<8 )
+ {
+ error("\nToo few columns, does not look like output of 'samtools pileup -c': $line\n");
+ }
+ my ($chr,$pos,$ref,$cons,$cons_qual,$snp_qual,$rms_qual,$depth,$a1,$a2) = @items;
+ $ref = uc($ref);
+ $cons = uc($cons);
my ($alt,$gt);
if ( $ref eq '*' )
{
# An indel is involved.
- if ($chr ne $prev_chr || $pos ne $prev_pos)
+ if ( $ignore_indels )
+ {
+ $prev_ref = $ref;
+ $prev_pos = $pos;
+ $prev_chr = $chr;
+ next;
+ }
+
+ if (!defined $prev_chr || $chr ne $prev_chr || $pos ne $prev_pos)
{
if ( !$$opts{refseq} ) { error("Cannot do indels without the reference.\n"); }
if ( !$refseq ) { $refseq = Fasta->new(file=>$$opts{refseq}); }
$ref = $refseq->get_base($chr,$pos);
+ $ref = uc($ref);
}
else { $ref = $prev_ref; }
- # One of the alleles can be a reference and it can come in arbitrary order
+ # One of the alleles can be a reference and it can come in arbitrary order. In some
+ # cases */* can be encountered. In such a case, look in the additional columns.
my ($al1,$al2) = split(m{/},$cons);
+ if ( $al1 eq $al2 && $al1 eq '*' ) { $al1=$a1; $al2=$a2; }
my $alt1 = parse_indel($al1);
my $alt2 = parse_indel($al2);
if ( !$alt1 && !$alt2 ) { error("FIXME: could not parse indel:\n", $line); }
- if ( $alt1 && $alt2 && $alt1 eq $alt2 ) { $alt2=''; }
if ( !$alt1 )
{
$alt=$alt2;
- $gt='0|1';
+ $gt='0/1';
}
elsif ( !$alt2 )
{
$alt=$alt1;
- $gt='0|1';
+ $gt='0/1';
}
- else
+ elsif ( $alt1 eq $alt2 )
+ {
+ $alt="$alt1";
+ $gt='1/1';
+ }
+ else
{
$alt="$alt1,$alt2";
- $gt='1|2';
+ $gt='1/2';
}
}
else
{
+ if ( $ignore_snps || (!$keep_ref && $ref eq $cons) )
+ {
+ $prev_ref = $ref;
+ $prev_pos = $pos;
+ $prev_chr = $chr;
+ next;
+ }
+
# SNP
($alt,$gt) = iupac_to_gtype($ref,$cons);
}
- print $fh_out "$chr\t$pos\t.\t$ref\t$alt\t$snp_qual\t0\t\tGT:GQ:DP\t$gt:$cons_qual:$depth\n";
+ print $fh_out "$chr\t$pos\t.\t$ref\t$alt\t$snp_qual\t0\tDP=$depth\tGT:GQ:DP\t$gt:$cons_qual:$depth\n";
$prev_ref = $ref;
$prev_pos = $pos;
sub Fasta::new
{
my ($class,@args) = @_;
- my $self = @args ? {@args} : {};
+ my $self = {@args};
+ bless $self, ref($class) || $class;
if ( !$$self{file} ) { $self->throw(qq[Missing the parameter "file"\n]); }
$$self{chr} = undef;
$$self{from} = undef;
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