recode bed file into raw data, but the genotype count does not follow the base data

Question

[Phylicia]

Hi, I use this code to recode bed file into raw data in ubuntu. I refer to the codes about Plink here

plink\
--bfile bedfile_name\
--recode A\
--recode-allele base_data.txt\
--out  output.txt

It says the "recode-allele" code should follow base_data.txt. The first column should be variant ID and the second column should be allele ID. I have tried column-name-free or not of base_data.txt.

But the results I got is different from my expectation. The bed file has been recoded successfully, but the effect allele does not follow the rule of the effect allele (the second column) defined in the base_data.txt.

Here is the example. The effect allele is C, but the effect allele of this allele in the output file is T.

What could I do? Thank you very much and look forward to your kind help.

[ATpoint]

Pro tip, rather than using all these irrelavant tags just use tag plink so the developer who is active here can easily spot it and help out (or others familiar with plink). You can use edit to change that.

[Phylicia]

Thank you very much！