bcftools annotate added most rs IDs, but not all.
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?
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your using the wrong database.vcf.gz
the database is incomplete (exome vs genome)