Question: How to extract the loci that has more than 2 alleles in PLINK dataset?
gravatar for leileicui_xuan
3.1 years ago by
leileicui_xuan0 wrote:

Sometimes when I generated a PLINK dataset by myself, the dataset will usually contains many loci that has >2 alleles and I wonder is there some commands in PLINK could check and extract out these bad loci? Many thanks!

ERROR: Locus SNP7 has >2 alleles: individual MAGIC MAGIC.101 has genotype [ A T ] but we've already seen [ A ] and [ G ]

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