bcftools / samtools, which database does the MAF function use?

Question

[Davide Chicco]

Hi

I am working with bcftools view to filter variants based on a specific MAF (minor allele frequency) cutoff.

It works well but there's an information I am missing: which database is bcftools using to apply the MAF filter, that is to claim if a variant is rare or not?

Thanks!

-- Davide

Answer 1

[Pierre Lindenbaum]

there is no database associated de facto with bcftools. It uses the AC/AN/AF from the genotypes in the VCF.

[Davide Chicco]

Hi Pierre

Thanks for the reply. Are you saying the information about if a variant is rare (or not) is present in the header of the VCF file we're using?

If yes, how does bcftools view retrieve it?

And, more important, how can we know which database did the people who generated the file used to state which variants are are and which variants are not?

Merci!