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Converting plink to GenEpi files

Hi hi I am a bioinf noob with 75% of my masters course work due in 9 days LOL I want to convert my hapamp1.bed/.bim/.fam to .gen for using the same data set in GenEpi.

This code$ plink-1.07-mac-intel/plink --bfile hapmap1 --recode oxford --out hapmap1

returns: ** Unused command line option: oxford

ERROR: Problem parsing the command line arguments.

Any ideas?

plink genepi
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updated by 4galaxy77 4galaxy77 • written by Mollie • Mollie

1 answer

You need to use a newer plink version (1.9 or 2.0).

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written by chrchang523 chrchang523

Legend, I'll try that now. Sorry for the dumb question lol

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written by Mollie • Mollie

I get this error: Error: Failed to open hapmap1.bed. Using: ./plink --bfile hapmap1 --recode oxford --out hapmap1

:/

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written by Mollie • Mollie

Do I need to convert the .ped and .map files to .bed?

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written by Mollie • Mollie

are you sure you are running the plink command from the directory that the .bim/.bed./.fam files are in? That error suggests you aren't.

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written by 4galaxy77 4galaxy77

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