Question: Error: --fst requires at least two nonempty clusters.
0
gravatar for msimmer92
22 months ago by
msimmer92150
Uruguay
msimmer92150 wrote:

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)

plink • 839 views
ADD COMMENTlink modified 22 months ago • written 22 months ago by msimmer92150

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 ?

ADD REPLYlink written 22 months ago by dschika290

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.

ADD REPLYlink written 22 months ago by msimmer92150
2
gravatar for msimmer92
22 months ago by
msimmer92150
Uruguay
msimmer92150 wrote:

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

ADD COMMENTlink written 22 months ago by msimmer92150

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

ADD REPLYlink written 19 months ago by rgiannico100

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

ADD REPLYlink written 8 months ago by mike229lin10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 720 users visited in the last hour