I have a vcf file of about 565 individuals. I want to replace the missing SNPs of one of them (Ancient sample) with the reference alleles.
I was thinking about trying out the following-
$ bcftools +fixploidy phasedVCF-short02.vcf.gz -- -f 2|bcftools +missing2ref - -- -p > phasedVCF-short03.vcf
But it will probably replace the missing sites in all the individuals.
I am bit confused if there is any function in vcftools or bcftools which would specify to do this operation in only one individual instead of all.