format error in the input file, --fastBAT gene-set GWAS,
Opened this issue · 3 comments
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!
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.
I am having the same issue. Did you find a solution? Thanks!!
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.