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voichek / kmersGWAS

A library for running k-mers based GWAS
GNU General Public License v3.0
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kmers---plink #26

Closed duhuipeng closed 4 years ago

duhuipeng commented 4 years ago

I'm using the Gemma run or the mistake I told you before, and I see this line of code on your manul.pdf,

bin/kmers_table_to_bed -t kmers_table -k 31-p phenotypes.pheno --maf 0.05--mac 5-b 10000000-o output_file, can use plink for subsequent GWAS association analysis, and I generate the following files: image then used plink analysis commands: plink --blife output_file.0 --assoc --out assoc_results Nevertheless, when his result comes out p the full value NA, can not draw a Manhattan map, what is the jie of this value

Looking forward to your reply

duhuipeng commented 4 years ago

image P value worthwhile results

voichek commented 4 years ago

I am not sure what is the problem with plink as I never used it to run associations. I can only help with the creation of the PLINK binary file. I usually used GEMMA to run associations on the plink binary file.