PLINK 1.9 can import data from Variant Call Format (–vcf), binary VCF (–bcf), and Oxford-format (–data, –bgen) files. However, since it cannot handle genotype likelihoods, phase information or variants with more than two alleles, the import process can be quite lossy. Specifically, With Oxford-format files, genotype likelihoods smaller than 0.9 are normally treated as missing calls, and the rest are treated as hard calls. –hard-call-threshold can be used to change the threshold, or request independent pseudorandom calls based on the likelihoods in the file.Phase is discarded.By default, when a VCF variant has more than one alternate allele, only the most common alternate is retained; all other alternate calls are converted to missing. –biallelic-only can be used to skip variants with multiple alternate alleles.
