Question about --indep-pairwise (plink v1.9)

[戴睿紘]

Hi there, 

I am reading a paper which use plink to LD-pruning.

They use PLINK to do

"LD-pruning on this subset of markers was performed with PLINK v.1.9, with an r2 threshold of 0.1 within a sliding window of 50 Kb and a shift step of 10 Kb"

However, I cannot figured out how to do this, espacially "sliding window of 50 Kb"
In plink website, the option --indep-pairwise <window size>['kb'] <step size (variant ct)> <r^2 threshold> did not allow sliding window of 50 kb.

I've tried to run with the following command:

plink --vcf ./Cb.8samples.vcf --make-bed -geno 0.999 -out $FILE --allow-extra-chr --indep 50kb 10kb 0.1

And I got error message:

Error: Invalid --indep window size '50kb'.

How do I do shift step of 10 Kb ?

Thank you.

Best regard,

Jui-Hung

[Christopher Chang]

Unfortunately, this option does not exist; the paper is misreporting what it did.  If you are trying to precisely reproduce their results, their actual command was probably either "--indep-pairwise 50 10 0.1" or "--indep-pairwise 50kb 10 0.1".

(As a practical matter, when specifying the window size in kilobase units, PLINK 2.0 forces you to set the step-size to 1, since this prevents some weird behavior without significantly slowing down the computation.  For the same reason, you should never use "--indep-pairwise 50kb 10 0.1" for any purpose other than trying to precisely reproduce old results.)

[戴睿紘]

Thank you for your response. While the answer is unfortunate for me, it has saved me valuable time in figuring things out.

Many thanks !

Best regards,
Jui-Hung

chrch...@gmail.com 在 2023年10月30日 星期一下午5:50:18 [UTC+8] 的信中寫道：