what is BCFtools" f_missing" removing?

Question

[mdav]

I'm a bit confused by BCFtools "f_missing" command, and what exactly it is removing? Eg. if using:

F_MISSING<0.1

is it removing individuals, or variants which have greater then 10% missingness?

Is someone able to help explain this command, as in the manual it just says "fraction of missing genotypes" but this isn't super clear to me on what exactly is being removed.

Thanks!

Answer 1

[Pierre Lindenbaum]

F_MISSING<0.1

fraction of missing genotypes (a missing genotype is a genotype only NO-CALL alleles . , like './.`).

https://samtools.github.io/hts-specs/VCFv4.3.pdf

If a call cannot be made for a sample at a given locus, ‘.’ must be specified for each missing allele in the GT field (for example ‘./.’ for a diploid genotype and ‘.’ for haploid genotype).