Question

Problem After Imputation From 1000 Genome

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12.3 years ago

Raha • 0

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 • 2.2k views

ADD COMMENT • link updated 10.4 years ago by Biostar 20 • written 12.3 years ago by Raha • 0

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Which software are you using?

ADD REPLY • link 12.3 years ago by Maxime Lamontagne ★ 2.3k

score 0 · Answer 1 · 2012-01-17

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12.3 years ago

Raha • 0

Mach and Minimac.

ADD COMMENT • link 12.3 years ago by Raha • 0

score 0 · Answer 2 · 2012-01-17

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.