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jianyangqt / gcta

GCTA software
GNU General Public License v3.0
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format error in the input file, --fastBAT gene-set GWAS, #78

Open wangxu1990 opened 5 months ago

wangxu1990 commented 5 months ago

For the --fastBAT, it is written in the official webpage "The input file test.ma has columns including SNP ID, the effect allele, the other allele, frequency of the effect allele, effect size, standard error, p-value and sample size“, but I only have two columns, one SNP, one P value. Does it come from the missing the other columns? but I did find that someone work well with the only two columns?

Thank you!

zakathornton commented 5 months ago

I am also getting the same error when using the following format:

SNP A1 A2 freq BETA SE P N rs144155419 A G 0.0105148 0.0184197527119345 0.0532524074964082 0.73 384695 rs58276399 C T 0.111021 0.00817875864795281 0.0176013547770624 0.64 375599 rs141242758 C T 0.110931 0.00792184774651085 0.0175842555059275 0.65 376684

I have also tried using whitespace rather than tab delimited, but I receive the same issue. Additionally, removing the header row gives the same error message.

M-luigi commented 3 months ago

I am having the same issue. Did you find a solution? Thanks!!

M-luigi commented 3 months ago

I just tried using a newer version of GCTA and it is reading the --fastBAT input file. The error was generated when using version 1.93, and it is working fine on version 1.94.