I have a genotype data vcf file of 100 individuals filtered for maf >.01 and then I take wgs file of another 50 individuals
and I intersect the sites that are common in both genotype and wgs data.
I merge the wgs and genotype data for these common sites using bcftools
This new merged vcf file has sites that have MAF of genotype file. How do I update the MAF in new merged vcf file?