This code in R takes a VCFR object as input and converts it to a 012 geno format

convert VCF to 012 format

 #pl_vcf is read in with VCFR package
 ext_vcfgt_num2 <- extract.gt(pl_vcf, as.numeric = FALSE) # extract the genotype matrix from the vcf fil
  str(ext_vcfgt_num2)
  # “0/0” --> 0
  # “0/1" or “1/0” --> 1
  # “1/1" is --> 2
  FirstAllele<- matrix(as.numeric(substring(ext_vcfgt_num2,1,1)), ncol=ncol(ext_vcfgt_num2)) #first character is first allele
  SecondAllele<- matrix(as.numeric(substring(ext_vcfgt_num2,3,3)), ncol=ncol(ext_vcfgt_num2)) #third character is second allele
  Genotype <- FirstAllele + SecondAllele
  str(Genotype)
  print(dim(Genotype))
  print(table(Genotype)) # counts of 0,1,2
  sum(is.na(Genotype)) # missing data
  hist(colSums(is.na(Genotype)), breaks=seq(0,10000,10), main=paste(vcf_obj[i],“Missing loci per individual”)) #histogram of missing data per individual
  hist(rowSums(is.na(Genotype)), breaks=seq(0,100,1), main=paste(vcf_obj[i],“Missing individuals per locus”)) #histogram of missing data per locus
  colnames(Genotype) <- colnames(ext_vcfgt_num2)
  rownames(Genotype) <- rownames(ext_vcfgt_num2)