convert genotype to allelic for plink

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7.5 years ago

alipanah.masoud • 0

hi

I am new in pink, my problem is convert my data for bed file, my dat form is ID AA AB AA BB ... about 20000, I haven't FID,MID, SEX I want the form ID A A A B B B. please write me linux command

thanks

software error • 1.5k views

ADD COMMENT • link 7.5 years ago by alipanah.masoud • 0

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What should happen to indels? Or is this from a SNP array? What should happen to missing genotypes?

In addition, what have you tried? It's good practice to first show us what you tried and how far you got.

ADD REPLY • link 7.5 years ago by WouterDeCoster 47k

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thanks WouterDECoster

I add space with R program but can't split using splitstackshope in plink when using compound genotype in last command line. I see following error "Problem with compound genotype [ B.B.1 ] should be two characters long"

ADD REPLY • link 7.5 years ago by alipanah.masoud • 0

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Please use ADD REPLY to answer to earlier posts, as such this thread remains logically structured and easy to follow.

In addition, I have no idea what splitstackshope is and what your error exactly means.

ADD REPLY • link 7.5 years ago by WouterDeCoster 47k

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