Assigning gene identifiers to SNPs with bcftools annotate

Question

[maxa]

Hello,

I have a VCF file with SNPs. It contains the chromosome and the position of the SNPs, but the ID column is empty (.). I want to fill the ID column with gene identifiers which i have in a tab-deliminated file with four columns: Chromosome, start position, end position, identifier. Let's call it coordinates.gff.

I used

bcftools annotate -a coordinates.gff.bgz -c CHROM,FROM,TO,ID -o variants_annotated.vcf -Ov --threads 2 variants.bcf

A tabix index exists for the coordinates file and there are no error messages. Still, the ID column of the output file is empty. I'm struggling with this for a while now and I have the feeling that I'm missing something very obvious. Do I have to specifiy that I want the IDs to be replaced in some way?

Any help would be highly appreciated!

[Pierre Lindenbaum]

same chromosome notation ? no +1 problem with the positions ?

Answer 1

[maxa]

I found the solution in another post here.

[bioblast]

It seems to me that the link you posted provides information on adding gene annotation information to the INFO column of the vcf, not the ID column. Is there a way you found to add it to the ID column?