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i want to know if plink is running prunning

Hi, I am pruning the SNP based on LD using the command --indep-pairwise 50 5 0.5.

However, I don't know how many percent have been finished.

Anyone know how to show the prune the results based on LD?

software-error
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updated by Ram Ram • written by rihou66 • rihou66

I tried to edit your question to be legible because it wasn't clear exactly what you were asking. Rather than check if the program is running, it sounds like you want to do some post-processing or find the usage of a plink sub-command? Please edit the post or comment if this is not correct. I was trying to help but I'm honestly still a little unclear. Checking if a command is finished is trivial with top or ps.

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written by SES SES

Sorry, I am using windows system, so I cannot check if a command is finished with top or ps.

I am doing LD based pruning using Plink v1.07, however, I cannot get the results. The files of prune.in and prune.out are blank. and I do not know if it is still in calculating.

• 0 views • link
updated by Ram Ram • written by rihou66 • rihou66

1 answer

log producted by plink as following :

Before frequency and genotyping pruning, there are 774 SNPs
Applying filters (SNP-major mode)
0 founders and 174 non-founders found
Writing list of removed individuals to [ plink.irem ]
4 of 174 individuals removed for low genotyping ( MIND > 0.1 )
Total genotyping rate in remaining individuals is 0.987103
27 SNPs failed missingness test ( GENO > 0.1 )
0 SNPs failed frequency test ( MAF < 0.01 )
After frequency and genotyping pruning, there are 747 SNPs

but I want to know the results of pruing based on LD

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updated by Ram Ram • written by rihou66 • rihou66

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