bcftools annotate added most rs IDs, but not all.

Question

[Kevin]

As the title suggests, I am using bcftools annotate (from here) trying to add all the rs IDs into my file, but many are still missing. I'm a computer science student trying my best to understand what all of this means, so any help is appreciated. Here are the reference files I'm using:

FASTA reference: human_g1k_v37 (from here)

.vcf.gz reference: 1000G_omni2.5.hg38.vcf.gz (from here)

Could it be that I'm not using the correct reference files for my given BAM data?

[Pierre Lindenbaum]

trying my best to understand what all of this means

• you have rare variants that were not already discovered in the database.vcf.gz

• your using the wrong database.vcf.gz

• the database is incomplete (exome vs genome)