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biocore-ntnu / snpflip

Report reverse and ambiguous strand SNPs in GWAS data
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duplicated SNP in the .reverse file #3

Open saintland opened 6 years ago

saintland commented 6 years ago

Hi there: I ran snpflip for each chromosome following the example. But I got a lot of duplicated SNP in the reverse file. Plink can't use it with duplicated SNPs. Can you take a look? chr19.reverse JHU_19.249356 JHU_19.249356 kgp12221412 kgp12221412 rs2312724 JHU_19.267212 rs11878315 rs12981067 rs3813154 rs1077446 rs1108414 rs4898158 rs76159277 rs4897943 exm1395440 rs7256434 rs7250095 JHU_19.322522 rs7256086 rs2166359 rs6510725 rs2044406 JHU_19.361941 rs3764656 rs113438119 JHU_19.364054 rs662923 rs73506558 JHU_19.369525 JHU_19.369525 ....

Thanks,

Han

endrebak commented 6 years ago

Could you try pip install snpflip==0.0.6 and see if I fixed it? Thanks for trying the tool and reporting a potential bug!

If the problem persists, you could send me your bim at endrebak85 gmail.com and I'll look into it.