Question: Why does genotype data change after genetic imputation?
0
gravatar for iamselewa
12 months ago by
iamselewa0
iamselewa0 wrote:

Hello,

I am trying to perform genetic imputation on TCGA genotype data so I can perform a GWAS-type analysis. I used the Michigan imputation server with Minimac4 to impute all chromosomes (see methods below for full description).

I noticed that after imputation, SNPs that were physically genotyped have changed/are inconsistent for many individuals. Why does this happen? Observed values should not be affected by imputation, I think. Any help is appreciated.

Thanks!

Methods: I downloaded the TCGA Affymetrix SNP6 data and reformatted it into PLINKv1.9 files. I removed SNPs with MAF < 1%, HWE < 1e-5, genotype/individual call-rate < 95%, and I flipped negative-stranded to positive strand with snpflip tool. I also removed ambiguous stranded SNPs. I also performed ancestral filtering to make sure I only have European samples. I used --recode vcf in plink to convert bed files to VCF files. For Michigan imputation server, I imputed with Phase1 v3 (no singletons) and choose the EUR population.

genotype imputation • 367 views
ADD COMMENTlink written 12 months ago by iamselewa0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 678 users visited in the last hour