PLINK basic command line usage

Question

[Phylicia]

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!

[Kevin Blighe]

Which version of PLINK are you using? These parameters are only available in certain versions.

[Phylicia]

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!

[Sam]

We were referring to this plink in our tutorial. Those are standard parameter, so it is likely that you are using something else?

[Phylicia]

Thanks! How could I check which version plink I used, and switch to the right version of plink?

Answer 1

[chrchang523]

"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.

[Phylicia]

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?

Answer 2

[Phylicia]

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!