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
Hello https://www.biostars.org/u/24526/ ,

there is another `bcftools` plugin that should do this:

    $ bcftools +fill-from-fasta input.vcf -- -c REF -f genome.fa > output.vcf

fin swimmer