Standalone filtration of a VCF/BCF for IBD analysis, runnable on its own or called by the HmmIBD workflow. Masks low-depth genotypes, (optionally) preserves original allele frequencies, recomputes AN/AC/AF, selects variant types / biallelic sites, and optionally thins to a variant cap. The filtered callset is emitted in the requested output_format: a compressed BCF (default), a bgzipped VCF, or the hmmibd-rs text genotype table (+ matching allele-frequency file).
This is a companion discussion topic for the original entry at github.com/broadinstitute/long-read-pipelines/FilterVcfForHmmIBD