transfer-filter

vk geno transfer-filter <vcf>

Generate a FORMAT field filter column (FT) and transfer filters applied within the FILTER column to the FT field. This utility is useful if variants are called individually (producing a single VCF) for samples and then later merged into a multi-sample VCF. It enables you to track which variant filters were applied to a specific sample rather than across a population. The following header line is added:

##FORMAT=<ID=GF,Number=1,Type=String,Description="Genotype Filter">

het-polarization

vk geno het-polarization <vcf>

Creates a new FORMAT field (HP) and "polarizes" or switches heterozygous genotypes based on genotype likelyhoods (GL) or Phred-scaled genotype likelihoods (PL). For example, a variant with 7 reads supporting a reference call and 1 read supporting an alternate allele might be called as a heterozygous genotype. However, in hermaphroditic species (e.g. C. elegans) where limited or no heterozygosity exists, it is much more likely that the genotype is homozygous reference. The HP FORMAT field will list one of the following depending on the change made:

• AA - A heterozygous genotype was switched to a homozygous reference genotype.
• AB - A heterozygous genotype remains a heterozygous genotype.
• BB - A heterozygous genotype was switched to a homozygous alternate genotype.

The following header line is added:

##FORMAT=<ID=HP,Number=1,Type=String,Description="Flag used to mark whether a variant was polarized">