);
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 $refseq;
my $ignore_indels = $$opts{snps_only} ? 1 : 0;
+ 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\tdata\n]
+ ;
+
while (my $line=<$fh_in>)
{
chomp($line);
if ( !$alt1 )
{
$alt=$alt2;
- $gt='0|1';
+ $gt='0/1';
}
elsif ( !$alt2 )
{
$alt=$alt1;
- $gt='0|1';
+ $gt='0/1';
}
else
{
$alt="$alt1,$alt2";
- $gt='1|2';
+ $gt='1/2';
}
}
else
($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;