FastaAlternateReferenceMaker

FastaAlternateReferenceMaker looks like it may be a simple way if you have variant sites and the goal is to make a new (haploid) reference that incorporates those variants.

If, on the other hand you are trying to reconstruct the (potentially diploid) genome of an individual (i.e. you actually have genotypes rather than just a list of variant sites and alleles), then you can use the rtg samplereplay command from RTG Core to generate the genome corresponding to a sample contained in a VCF. For diploid chromosomes you will get two copies of each chromosome output. (You can also use samplereplay to generate a haploid alternate reference by representing your input data as a haploid sample containing all the variants, although there is not currently the option to output heterozygous SNPs with IUPAC ambiguity codes).