vcftools to update vcf with gene info from bed

[cmccabe]

I am trying to add gene information to a vcf file using vcftools:

vcftools annotate \
  -a genes.bed.gz \
  -c CHROM,FROM,TO,GENE \
  -h <(echo '##INFO=<ID=GENE,Number=1,Type=String,Description="Gene name">') \
  TSVC_001.vcf.gz

genes.bed.gz is compressed using bzip, sorted, and indexed by tabix

for f in /home/cmccabe/Desktop/tabix/*.bed ; do
    bname=$(basename $f)
    vcf-sort $f | bgzip -c > $f.gz ; tabix -p bed $f.gz
done

genes.bed.gz

chr1	955543	955763	AGRN
chr1	957571	957852	AGRN
chr1	970621	970740	AGRN

The vcftools command runs but I do not see that the vcf.gz was updated with the gene information from the bed file. Thank you .