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jianyangqt / gcta

GCTA software
GNU General Public License v3.0
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Problems with mtCOJO #82

Open Zhangzzzzzy opened 5 months ago

Zhangzzzzzy commented 5 months ago

When I try to run mtcojo, the following error is reported, but when I check my data, there are no duplicates of SNPs, and I don't know what the reason is.

**Accepted options: --mbfile test.txt --mtcojo-file gwas.txt --ref-ld-chr eur_w_ld_chr/ --w-ld-chr eur_w_ld_chr/ --out test_result

There are 1 PLINK genotype files specified in [test.txt].

Reading the PLINK FAM files .... 503 individuals have been included from the PLINK FAM files. Reading the PLINK BIM files ... 8550156 SNPs to be included from PLINK BIM files.

Reading GWAS summary data from [gwas.txt] ... Error: Duplicated SNP ID found: .. An error occurs, please check the options or data**

The text of my test.txt reads: EUR The text of my gwas.txt reads: drink test1.txt smoke test2.txt

anglixue commented 5 months ago

It seems the duplicated SNP ID is a single dot. This happened when rsID was not found so people use a single dot to represent the SNP id Assume your gwas object is called df and the SNP id column as SNP You might want to check sum(df$SNP==".")