How can we convert Allele column of Hapmap SNP genotype data format into ALT and REF columns of VCF format? In HapMap format, there is a column with header name allele. But in the vcf format, ALT and REF headers are present instead of allele headers like in hapmap. The Allele column contains A/C or C/G etc in HapMap. I want to know which base is the reference base A or C in A/C, C or G in C/G. But in vcf , ALT and REF columns are filled with single bases, either C, T, A or G. My question is, how can i convert Allele columns of hapmap format (A/C or C/G) into vcf ALT and REF alleles. Which allele of HapMap format, should i write as ALT and which allele as Ref. Actually, I want to convert allele column of HapMap format to ALT and REF alleles of VCF format. Is the first allele of HapMap, the allele of reference genome? Like, in C/G, C may be reference allele and G may be ALT allele or reverse. Does it follow any order like first one is reference allele and second is ALT allele or reverse will be the case? Thanks in Advance
