If you are not able to detect gender from array data using Xchromosome, what does it mean? Or should we subset the data to detect?

Alagu Sankareswaran @Alagu-Sankareswaran-2

31 May 2021 1 8K Report

I was trying to match the true gender and gender detected from the X-chromosome data from the Illumina bead chip array. However for many of the samples plink is not able to detect gender, predominantly for female samples? How to resolve such an issue. I would like to do X-chromosome imputation later in the Michigan Imputation server

Alagu Sankareswaran

Hi, Anna Wolc I have used Illumina genome studio to estimate gender. It is more accurate as it uses intensity and both X and Y in determining sex. But I want to use my data for X-chromosome imputation. Michigan imputation server relies on gender estimation from X-chromosome heterozygosity as done in plink.. When sex is undetected in plink for particular samples that means there is no clear cutoff between sexes for those undetected.

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