Plink Flag? I Have A Dataset That Is Formatted Weirdly And I Keep Getting An Error. How Do You Use The Flags?

Question

[Joe]

Hello so I type the following

plink --file FILE --compound-genotypes --missing-genotype N --allow-no-sex

and I get the following error

Writing this text to log file [ plink.log ] Analysis started: Fri Feb 08 20:28:34 2013

Options in effect: --file FILE --compound-genotypes --missing-phenotype N --allow-no-sex

30 (of 30) markers to be included from [ FILE.map ]

ERROR: Locus rs10059456 has >2 alleles: individual 12 NA18135 has genotype [ N N ] but we've already seen [ C ] and [ T ]

Any ideas?

Answer 1

[zx8754]

Try:

plink --file FILE --compound-genotypes --missing-genotype N --allow-no-sex --missing-phenotype

It would be helpful if you could give us sample file:

cut -f1-10 -d" " myfile.ped | head
head myfile.map