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Problem After Imputation From 1000 Genome

I used 1000 Genome phase 1 for my imputation. When it was finished, I noticed in "*.info.draft" files that for a lot of variants allele1 and allele2 are the same and the allele frequency is not 1.0. Could anyone let me know why does it happen and how I can solve the problem?

imputation genome
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updated by Biostar Biostar • written by Raha • Raha

2 answers

Mach and Minimac.

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written by Raha • Raha

I can't say why this is happening, but I got the same situation with one of my project. But it's only happening with C and G allele.

In my opinion, your results are good. MaCH probably see two different patterns with some monomorphic snp. Since allele1 and allele2 are the same, your imputed snps will still be monomorphic.

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written by Maxime Lamontagne Maxime Lamontagne

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