I am looking for a tool/script/pony to correct the REF column in a vcf file whenever that nucleotide doesn't match the reference genome, as supplied in fasta format.
It sounds like a common task but I could not find something. I did find bcftools +fixref but that only works for SNPs. My vcf files are from structural variants.
Cheers,
W
•
written
by
WouterDeCoster
Some code like this can help, but be aware that changing the reference column affects other fields in your VCF, such as the GT value.
#!/usr/bin/perl
use strict;
use warnings;
$ARGV[2] or die "use fixRefVCF.pl <GENOME_FASTA> <VCF> <FIX_VCF>\n";
my $genome = shift @ARGV;
my $orig_vcf = shift @ARGV;
my $new_vcf = shift @ARGV;
my %seq = ();
my ($chr, $pos, $ref, $obs);
warn "loading genome sequence from $genome\n";
open (my $fh, "<", $genome) or die "cannot read $genome\n";
while (<$fh>) {
chomp;
if (/>(\w+)/) {
$chr = $1;
} else {
$seq{$chr} .= $_;
}
}
close $fh;
open (my $vh, "<", $orig_vcf) or die "cannot read $orig_vcf\n";
open (my $oh, ">", $new_vcf) or die "cannot write $new_vcf\n";
while (<$vh>) {
if (/^#/) {
print $oh $_;
} else {
chomp;
my @var = split (/\t/, $_);
$chr = $var[0];
$pos = $var[1]; # VCF is 1-based, Perl string is 0-based
$ref = $var[3];
$obs = substr($seq{$chr}, $pos - 1, length $ref);
if ($ref ne $obs) {
warn "editing $chr:$pos $ref->$obs\n";
$var[3] = $obs;
}
print $oh join "\t", @var;
print $oh "\n";
}
}
close $vh;
close $oh;
Thanks! That seems to work beautifully well (and fast too).
Two comments: the warn "editing $chr:$pos $ref->$obs\n"; is off-by-one and the header is not written to the new vcf file ;-)
This script is nice to identify the variants whose REF allele is not correct and should be revised. It should be not used to change the reference alllele forcely with this script.
Ehm yes it should change those. That is exactly what I asked for.
So next step is apply plink --a1-allele to change the reference allele?
I did not use or need plink. I needed to modify the reference allele in a vcf file.
So what's the approach for you to modify the reference allele in a vcf. I find there are ~12% SNPs are REF/ALT reversed.
THIS SCRIPT FIXES THE REFERENCE ALLELES in a vcf file which are not correct when compared with a fasta file.
Hello WouterDeCoster ,
there is another bcftools plugin that should do this:
$ bcftools +fill-from-fasta input.vcf -- -c REF -f genome.fa > output.vcf
fin swimmer
This is the python solution I came up with, using cyvcf (minimally requiring v0.10.2) and pyfaidx. It can use compressed vcf and fasta files.
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tagging: Pierre Lindenbaum
what does it currently look like in the REF/ALT column ? (why do you need to fill the REF column (thinking of a very large deletion...) in your downstream analysis ? )
My main issue is that EVA complains that the nucleotides are incorrect. It seems their software only uses POS to check the REF nucleotide, and not END.
Just some lines from the vcf:
Essentially a single nucleotide would be sufficient - and in one file 98% is correct. The other file has
Nfor every position so some more changes need to be made.I'm already working on a python script (now posted as answer) but I thought someone else should have done it already ;p
For your narrow purpose, where all your insertions are symbolic rather than explicitly spelled out, the existing answers should be a satisfactory workaround to "bcftools +fixref"'s insistence on SNP-only data.
However, it's worth noting that there is a very good reason that bcftools insists on only SNPs. It's actually impossible to fix ordinary short indels: the only difference between a 1-base deletion and an insertion of the same base at the same position is the REF/ALT order.