Question

Converting plink to GenEpi files

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3.5 years ago

Mollie ▴ 10

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 • 954 views

ADD COMMENT • link updated 3.5 years ago by 4galaxy77 2.9k • written 3.5 years ago by Mollie ▴ 10

score 0 · Answer 1 · 2021-06-11

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3.5 years ago

chrchang523 11k

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

ADD COMMENT • link 3.5 years ago by chrchang523 11k

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

ADD REPLY • link 3.5 years ago by Mollie ▴ 10

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

:/

ADD REPLY • link 3.5 years ago by Mollie ▴ 10

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

ADD REPLY • link 3.5 years ago by Mollie ▴ 10

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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.

ADD REPLY • link 3.5 years ago by 4galaxy77 2.9k