BLINK GWAS output with weird format

[Rômulo Carleial]

 Dear all,
I am attempting to run BLINK using plink bed files as follows:
./blink_linux --gwas --file dataset --plink

The gwas result output is clearly wrong i.e. the table is not correctly formated, and the labeling is off:

taxa    chr     pos     maf     p_value

Qrob_Chr01:32864        0       0       7.889126e-02    8.634954e-01

Qrob_Chr01      32864   0       4.594883e-01    6.277502e-01

Qrob_Chr01:32873        0       0       8.386638e-02    5.722849e-01

Qrob_Chr01      32873   0       1.965174e-01    7.072825e-01

Qrob_Chr01:32880        0       0       1.133618e-01    1.414577e-01

Qrob_Chr01      32880   0       4.786780e-01    8.747994e-01

Qrob_Chr01:32912        0       0       2.274343e-01    1.461827e-01

As you can see, some information of the first snp appears on the following row, and so forth.

Can you please help me out with this? The .map file generated by BLINK looks absolutely fine:

rs      chr     pos

Qrob_Chr01:32864        Qrob_Chr01      32864

Qrob_Chr01:32873        Qrob_Chr01      32873

Qrob_Chr01:32880        Qrob_Chr01      32880

Qrob_Chr01:32912        Qrob_Chr01      32912

Qrob_Chr01:32934        Qrob_Chr01      32934

[許博程]

Hello, 

I encountered similar problems as you described here, and I run --vcf mode.

Rômulo Carleial 在 2023年11月9日 星期四晚上11:53:11 [UTC+8] 的信中寫道：

[許博程]

Hello everyone,

I found how can you fix this problem, which is recoding the chromosome name to the numerical numbers! Although this line posted last year, my discovery may not help the author of the post. I hope that my discovery will  help others who have similar question.

許博程 在 2024年10月23日 星期三下午5:28:15 [UTC+8] 的信中寫道：

[Rômulo Carleial]

Many thanks. Do you mean changing chromosome names to numbers? Like 1, 2 etc?