Hey, I am new to PLINK. I run a tutorial of how to calculate polygenic risk score under a tutorial.
https://choishingwan.github.io/PRS-Tutorial/target/#standard-gwas-qc
I run the part of # Standard GWAS QC and the code is as follows:
plink \
--bfile EUR \
--maf 0.01 \
--hwe 1e-6 \
--geno 0.01 \
--mind 0.01 \
--write-snplist \
--make-just-fam \
--out EUR.QC
I got the alarming as follows:
plink: unknown option "--bfile"
plink: unknown option "--maf"
Someone suggests there are two plink which are based on commend line and GWAS tool package plink, respectively. But I do know the differences between the two and how to use them, respectively.
How could resolve this bug? Thanks!
"Someone suggests there are two plink which are based on commend line and GWAS tool package plink, respectively."
More precisely, there is a totally different "PuTTY Link" program (https://system.cs.kuleuven.be/cs/system/security/ssh/introduction/putty/doc/Chapter7.html ) that is also called "plink" on the command line. That's what was invoked here. You need to install and run the GWAS tool package instead.
Thanks a lot, chrchang523! How could I install and run the GWAS tool package? Do I need to withdraw the previous version of plink first and how?
Hi guys, I have debuged.
I follow the tutorial and re-install the plink.
If I used whereis plink. I found the other plink in the /usr/bin.
Actually, the plink I suppose to use is in the /home/siyu/
Then I change the code into
/home/plink \
--bfile EUR \
--maf 0.01 \
--hwe 1e-6 \
--geno 0.01 \
--mind 0.01 \
--write-snplist \
--make-just-fam \
--out EUR.QC
Then I debug.
Thanks so much, your guys!
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Which version of PLINK are you using? These parameters are only available in certain versions.
https://www.cog-genomics.org/plink/1.9/general_usage
I downloaded plink from this website. Moreover, the ubuntu system inquiry me whether I need to install plink when running a code, then I copy the commend to install the plink. Thus, I do not know my version clearly. Thanks!
We were referring to this plink in our tutorial. Those are standard parameter, so it is likely that you are using something else?
Thanks! How could I check which version plink I used, and switch to the right version of plink?