Negative values for imputed genotypes on X chromsomes in females
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2.7 years ago
Caragh ▴ 40

Hi there,

I imputed a set of around ~10k individuals using the sanger imputation server (1000 Genomes Phase 3 with eagle and PBWT). The autosomal data looks perfect - passed QC fine. However, I am was QCing the X chromosome data and I noticed for pretty much all the SNPs in females there is negative genotype values in the gen file format (e.g. 1 0 -1). Has anyone come across this before? From what I can tell online this indicates very poorly imputed data and should be excluded. Is this the case?

If so - is there any way to improve the imputation quality for the X chromosome? After QC, (SNPs were screened for geno 0.1 and maf 0.01), there was approximately 24k SNPs in the genotype file put forward for imputation.

Many thanks for your help!

Caragh

imputation X X chromosome genotypes • 737 views
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