I have a filtered VCF file of mtDNA genotypes for multiple individuals. The calls are haploid and therefore the genotype field in the VCF is either 0 or 1. I would like to call consensus fasta files for each individual. However, it is my understanding that tools like
vcf-consensus and GATK's
FastaAlternateReferenceMaker apply all ALT variants to the reference fasta to obtain the consensus.
How can I generate consensus sequencess where the the ALT allele is assigned if the GT field is 1 and the REF allele if the GT field is 0?
Thanks in advance.