Question: Plink Flag? I Have A Dataset That Is Formatted Weirdly And I Keep Getting An Error. How Do You Use The Flags?
0
gravatar for Joe
6.0 years ago by
Joe0
Joe0 wrote:

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?

plink • 1.7k views
ADD COMMENTlink modified 6.0 years ago by zx87547.1k • written 6.0 years ago by Joe0
0
gravatar for zx8754
6.0 years ago by
zx87547.1k
London
zx87547.1k wrote:

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
ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by zx87547.1k
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