When converting .ped, .bim and .fam files to .pgen, .psam and .pvar in PLINK2
When we convert plink 1.9 file formats to plink 2, how in .pvar file recognises which allele is alternative and which is the reference. Because, in .bim file we do not have columns for alternative and reference alleles, separately. It has only two columns for allele 1 and allele 2. Please help me to understand this.
Thanks a lot.
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