How to correct invalid genotype in ped file ?
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6.9 years ago
deepue ▴ 150

Hi,

I would like to understand the protocol given in an article with the supplementary data. I could see there is an invalid genotype present in those files, there was no mention about correcting the data for the same in that protocol.

650 A651 0 0 1 1 T T C G A A 0 N
652 A653 0 0 1 1 T T C G A A 0 N
782 A783 0 0 1 1 T T G G G A 0 N
905 A906 0 0 1 1 C T G G A A 0 N


How to correct the invalid genotype(0 N) to missing genotype(0 0). Is there any option in plink itself, instead of command-line like options?

plink SNP genotype • 2.8k views
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What about the --output-missing-genotype option in plink? According to their manual: "Also, if --output-missing-genotype is specified (which can be as well as --missing-genotype) then this value [i.e. 0] will be used instead (i.e. so that input and output files can have different missing codes; this also applies to the phenotype with --output-missing-phenotype and --missing-phenotype)."