Error: --fst requires at least two nonempty clusters.

Question

[msimmer92]

Hello, i'm trying to calculate --fst values on a vcf that comprises the 1000genomes individuals and one sample of my own. i'm trying to do the following analysis:

plink --vcf todos41.vcf --within IDsparahw.txt --fst --make-bed --out todos41fst

But it gives back the following error: Error: --fst requires at least two nonempty clusters.

Any thoughts about what this means? Thanks !

PS: the IDsparahw.txt file has the following format:

head IDsparafreqs.txt 
1_HG00096 1_HG00096 EUR
2_HG00097 2_HG00097 EUR
3_HG00099 3_HG00099 EUR
4_HG00100 4_HG00100 EUR
5_HG00101 5_HG00101 EUR
6_HG00102 6_HG00102 EUR
7_HG00103 7_HG00103 EUR
8_HG00105 8_HG00105 EUR
9_HG00106 9_HG00106 EUR
10_HG00107 10_HG00107 EUR
...

(matching the header ID names from the vcf that's being used)

[dschika]

I have to admit that I have not used plink with --fst before. Therefore, this is just a guess from the error message: Is it possible that you did not define a second cluster in IDsparahw.txt file except of EUR ?

[msimmer92]

I defined several clusters. If you see the file you can see 7, so I don't know what's really the problem :/ . The clusters are: AFR, AMR, EUR, EAS, SAS , IND and AFURU.

Answer 1

[msimmer92]

Ok i solved it just now ! I had to put the --double-id flag :P

[rgiannico]

I had the same problem, and I solved it with the "--double-id" flag too. Thanks!

[mike229lin]

Does anyone think that the manual of PLINK is not easy to understand?

[dre.gaudio]

Hi, I have the same problem posted (cluster file similar to the posted one). Even when using --double-id flag. the result is always "Error: --mh/--bd requires at least two valid clusters."

Any clue? I cannot find anything useful in plink documentation. Thanks