The idea of state space reduction can be applied not only to improve HMM implementation efficiency but also to store large reference panels using less disk space. We introduce the m3vcf (minimac3 VCF) format, which is compatible with the Variant-Call Format (VCF) format. m3vcf files save each genomic segment in series where each segment has the list of bi- and multiallelic variants in order along with the unique haplotypes at these variants and a single line at the beginning of the block that describes which individual maps to which unique haplotype. This format reduces disk space requirements because it saves only the unique haplotypes at each block rather than all the haplotypes. The way in which the unique haplotypes are ordered (along columns) creates long runs of 0's and 1's (as they are ordered lexicographically from the first variant to the last variant) and is thus even more helpful in disk space reduction when using standard file compression methods such as gzip.
