I'm annotating whole genome VCFs with dbSNP identifiers with the following command:
bcftools annotate -a "indexed VCF.gz" -c ID "target indexed VCF.gz" > "output.vcf"
this works perfectly, but takes about 15 minutes on our server (all data on ssd based partitions). For small target VCFs containing for example a target region on chrY it helps to add the region to the command with -R regions.txt, but not for larger genome wide VCFs.
Is there any way to speed up the annotation process?