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Problem with output file plink GWAS

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Top Forums Shell Programming and Scripting Problem with output file plink GWAS
# 1  
Old 06-12-2014
Problem with output file plink GWAS
hi,

Can anybody help me about the odd output file yielded by the following command:

Code:
plink --noweb --allow-no-sex --bfile input_file --assoc --adjust --out output_file

In fact, I'd like to perform a simple Bonferroni basic association test, and I obtains the following output file (extract for first ten rows):

Code:
 CHR         SNP      UNADJ         GC       BONF       HOLM   SIDAK_SS   SIDAK_SD     FDR_BH     FDR_BY
   1   rs7540001        INF        INF        INF        INF        INF        INF        INF        INF 
   1   rs2743476        INF        INF        INF        INF        INF        INF        INF        INF 
   1   rs9435653        INF        INF        INF        INF        INF        INF        INF        INF 
   1  rs11810307        INF        INF        INF        INF        INF        INF        INF        INF 
   1  rs12410470        INF        INF        INF        INF        INF        INF        INF        INF 
   1   rs2873038        INF        INF        INF        INF        INF        INF        INF        INF 
   1   rs1553451        INF        INF        INF        INF        INF        INF        INF        INF 
   1   rs2580567        INF        INF        INF        INF        INF        INF        INF        INF 
   1  rs11578605        INF        INF        INF        INF        INF        INF        INF        INF 
   ....
   ....

This file contains (528000 rows (SNPs)), in particular: 328 rows with BONF = "INF", and 1300 others rows with BONF < 0.05, the remaining SNPs present a higher BONF-value than 0.05.
My question is: 1300+328 = 1628 (huge) is really the number of SNPs declared significants (<0.05) ? is it normal to get this kind of file ?

Thanks for you
Moderator's Comments:
Mod Comment Please use CODE tags when displaying sample input, output, and code.
Last edited by Don Cragun; 06-12-2014 at 03:18 PM.. Reason: Change BOLD tags to CODE tags and add CODE tags for sample output.
# 2  
Old 09-03-2014
I have the same problem with my results. Anyway, I wonder if you know how to draw the dendrogram tree according the cluster results? I used IBS cluster function and I got the *.cluster3 file, I want draw a tree according to the results. Anyone can help?
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