Recode VCF file according to ancestral alleles (AA)
1
1
Entering edit mode
5.3 years ago
abascalfederico ★ 1.1k

I am working with 1000G vcf files. These files contain an AA field indicating which is the Ancestral Allele. I would like to use this information to recode the vcf file. When the REF allele is different from the AA,  REF and ALT alleles should be switched,  AF fields recalculated (derived AF=1-AF), and genotypes be properly recoded (1/1 --> 0/0, 0/1 --> 0/1...).

Are you aware of any tool doing this? If there were no such tool, I would probably try myself and share the script here.

Thanks!

Federico

VCF • 2.9k views
ADD COMMENT
2
Entering edit mode
5.3 years ago
abascalfederico ★ 1.1k

Here is the solution I (dirty) coded - in case it is useful to others.

while(<>) {
    if(/^#/) {
        print $_;
        next;
    }
    chomp;
    my($chr,$site,$rs,$ref,$alt,$info) = (split(/\t/,$_))[0,1,2,3,4,7];
    my $ancestral_allele;
    $ancestral_allele = (split(/AA=/,$info))[1];
    $ancestral_allele = (split(/\|/,$ancestral_allele))[0];
    $ancestral_allele = uc($ancestral_allele);
    if($ancestral_allele !~ /[ACGT]/) {
        print STDERR "Ancestral allele ($ancestral_allele) is not ACGT: $_\n";
        $ancestral_allele = $ref;
    }

    if($ancestral_allele eq $ref) { #ok as it is
        print "$_\n";
        next;
    } else { #Switch alleles
        my @tmp = split(/;/,$info);
        foreach my $t ( @tmp ) {
            next if($t !~ /AF/);
            my($key,$val) = split(/=/,$t);
            my $new_AF = 1-$val;
            $_ =~ s/$key=$val/$key=$new_AF/;
        }
        @tmp = split(/\t/,$_);
        my $str = "";
        foreach my $t ( @tmp ) {
            if($t =~ /^[01][\|\/][01]/) {
                my($a,$b) = (split(/\|/,$t))[0,1];
                if($a == 0)    {    $a = 1;    }
                elsif($a == 1) {    $a = 0;    }
                if($b == 0)    {    $b = 1;    }
                elsif($b == 1) {    $b = 0;    }
                $t = "$a|$b";
            }
            $str .= "$t\t";
        }
        $str =~ s/\t$//;
        print "$str\n";
    }
}
ADD COMMENT
0
Entering edit mode
I made a post here, could you also help me answer it. Thank you very much. Ancestral Allele for the Genus Gallus
ADD REPLY

Login before adding your answer.

Traffic: 2251 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6