Unused command line option: --make-just-fam
We are trying to run the plink command for QC
plink \
--bfile EUR \
--maf 0.01 \
--hwe 1e-6 \
--geno 0.01 \
--mind 0.01 \
--write-snplist \
--make-just-fam \
--out EUR.QC
however, it gives us an error: ERROR: Problem parsing the command line arguments. Please what may be the possible cause of the error. I am using the Cygwin platform on windows.
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davidenoma •
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suraj.adewale1 •
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written
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suraj.adewale1 •
2 answers
That error message is from plink 1.07. This flag requires plink 1.9.
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chrchang523
I tried the issue on my virtual machine and it turns out that you have to install the plink 1.90 beta version from https://www.cog-genomics.org/plink/
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davidenoma •
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Can you at least show the full error log?
This is the full error output from plink. only that
** Unused command line option: --make-just-fam