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11 weeks ago
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Hi! I am trying to make a VCF file from .ped and .map files from an illumina MEGA array (two sets, each one having some of the samples I need for my analysis). At first I thought this was straightforward just using PLINK, but looking at the SNP Table, I am realizing that this conversion will be more complicated due to the TOP/BOT and +/- strand designations. I think my SNP Table is already in TOP format, but the SNPs are not all on the same strand as the reference, which I need them to be. How do I navigate this system to make my VCF file?
