PLINK --within flag not clustering all of the samples

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7.6 years ago

aritra90 ▴ 70

Hi All,

I have a clst.dat file in PLINK which has FID IID CLSTID format. I have 10 clusters, but after I run the following:

./plink --bfile Filename --freq --within clst.dat --out FileOut

The log says only 7 clusters were loaded, covering 43 people. However, I have 370 people covered in 10 clusters. I am wondering what am I missing or do I have to use any QC technique to get all the people in all clusters.

I am doing this to generate the frq.strat file to input in TREEMIX.

Any help is appreciated.

Thanks

PLINK genotype clustering treemix • 2.6k views

ADD COMMENT • link 7.6 years ago by aritra90 ▴ 70

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Hi,

Can you send me the .log file from that run, along with Filename.fam and clst.dat?

ADD REPLY • link 7.6 years ago by chrchang523 10k

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Hi,

Should I mail you at chrchang@alumni.caltech.edu ? Please let me know otherwise.

Thanks a lot for the prompt response.

ADD REPLY • link 7.6 years ago by aritra90 ▴ 70

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Yes, that should work.

ADD REPLY • link 7.6 years ago by chrchang523 10k

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Hi,

I have mailed you all the files but got a failure mail from the mail delivery system saying probably it's over quota. It'd be great if you look into it or if you have an alternate email.