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
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. At a later time I want to use those gene names to filter the vcf. Thank you .